Running as unit: rb-build-amd64_11-67713.service; invocation ID: c0ba226aa17841afb34611a3bbb53a63 ==================================================================================== Tue Sep 16 09:34:32 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job reproducible_builder_amd64_11) on jenkins, called using "ionos1-amd64 ionos15-amd64" as arguments. Tue Sep 16 09:34:32 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-7L1hdYDI" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 16 09:34:32 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Tue Sep 16 09:34:32 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-3yyANr' Tue Sep 16 09:34:32 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Tue Sep 16 09:34:32 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-WlLLwx' ok, let's check if libbpp-seq is building anywhere yet… ok, libbpp-seq is not building anywhere… UPDATE 1 ============================================================================= Initialising reproducibly build of libbpp-seq in unstable on amd64 on jenkins now. 1st build will be done on ionos1-amd64.debian.net. 2nd build will be done on ionos15-amd64.debian.net. ============================================================================= Tue Sep 16 09:34:55 UTC 2025 I: starting to build libbpp-seq/unstable/amd64 on jenkins on '2025-09-16 09:34' Tue Sep 16 09:34:55 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/67713/console.log 1758015295 amd64 unstable libbpp-seq Tue Sep 16 09:34:55 UTC 2025 I: Downloading source for unstable/libbpp-seq=2.4.1-13 --2025-09-16 09:34:55-- http://deb.debian.org/debian/pool/main/libb/libbpp-seq/libbpp-seq_2.4.1-13.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2169 (2.1K) [text/prs.lines.tag] Saving to: ‘libbpp-seq_2.4.1-13.dsc’ 0K .. 100% 253M=0s 2025-09-16 09:34:55 (253 MB/s) - ‘libbpp-seq_2.4.1-13.dsc’ saved [2169/2169] --2025-09-16 09:34:55-- http://deb.debian.org/debian/pool/main/libb/libbpp-seq/libbpp-seq_2.4.1-13.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2169 (2.1K) [text/prs.lines.tag] Saving to: ‘libbpp-seq_2.4.1-13.dsc’ 0K .. 100% 253M=0s 2025-09-16 09:34:55 (253 MB/s) - ‘libbpp-seq_2.4.1-13.dsc’ saved [2169/2169] Tue Sep 16 09:34:55 UTC 2025 I: libbpp-seq_2.4.1-13.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libbpp-seq Binary: libbpp-seq-dev, libbpp-seq12t64 Architecture: any Version: 2.4.1-13 Maintainer: Debian Med Packaging Team Uploaders: Julien Dutheil , Andreas Tille Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/libbpp-seq Vcs-Git: https://salsa.debian.org/med-team/libbpp-seq.git Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), cmake, d-shlibs (>= 0.106~), libbpp-core-dev Package-List: libbpp-seq-dev deb libdevel optional arch=any libbpp-seq12t64 deb libs optional arch=any Checksums-Sha1: a79687bdf2ce4c5c2031cb5da8394a9420804f90 322620 libbpp-seq_2.4.1.orig.tar.gz d826033655a203f1e71505464901b96e073dbf1e 12244 libbpp-seq_2.4.1-13.debian.tar.xz Checksums-Sha256: dbfcb04803e4b7f08f9f159da8a947c91906c3ca8b20683ac193f6dc524d4655 322620 libbpp-seq_2.4.1.orig.tar.gz 3e0b877ccae3846f83e0ed86546c5c475fc6107729aa58e203c6f2792aeeb56d 12244 libbpp-seq_2.4.1-13.debian.tar.xz Files: bdafc80aab9591ff79556138d6555941 322620 libbpp-seq_2.4.1.orig.tar.gz 52dec0368bb77da4a9af7983e03ab13c 12244 libbpp-seq_2.4.1-13.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmazN+ERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE7MhAAhwuIuD8ZvxSHwCRhnz7yKONGDxnhfqqe bVJZ7xaytV2OUqCil2AqtMJ8cjLwB6s8WSsOUrGZGh3a7ydHi/LWBf44DuCch1bg 4xcb5RZKgPkkTnKWBHaeuUXjoCmu4UI+JsMCb6CZsU19HrrZux2ENYkI8Y6RNDSV +B6ep3R1mbnmIEiiQQRNrtg4tpgJijPmWxnFeQYhSYkIaYocYhZSBjEwXCruBAsI NPKq8LrlYdtBQxxuQQyij1mIxjSTRa1zKXj/QNMuM6Z4d/hW8neimiOWYQdFcPqi z5hoAix/Q5HSbeMBKNw7PQBViYHOJtLyLLtBkPyxI3ML15MAPsU6NfbyAj5JqBbg i61uTSZWWx+NgGqjNXbo38FXeD+hDijt0qCnpRHTFBKqM59z9oXOQVQ83Hjr95rc sleGahi5zKbHsYMFCYCHWmk5o5eMAtbC3ESSbQmo5gymWOczZE9EUf2Gm1sQZROB T7qxEijZnEWdmMmTmBNqKD3b0ghNsO4bi/CidNb5/w8l/VYOJBKAnswz6uGQwQTz lU9Kl0pY/D9dS+Ft3vDH4ND1ZjVbcTJnIY2b6o0ICtKzPQNWPzvqNpxacuBT0rEt MJx8bt+Wk498ABxG3Pm3aLdbfsWLV+y9Bfo+s52ZmZIg8ZUlH/98/UqmGimFVUXB EfswTPNAAd0= =jZSB -----END PGP SIGNATURE----- Tue Sep 16 09:34:55 UTC 2025 I: Checking whether the package is not for us Tue Sep 16 09:34:55 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Tue Sep 16 09:34:55 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Tue Sep 16 09:34:55 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos1-amd64.debian.net is marked as down. Tue Sep 16 09:34:55 UTC 2025 - checking via ssh if ionos1-amd64.debian.net is up. removed '/tmp/read-only-fs-test-14fKay' ==================================================================================== Tue Sep 16 09:34:55 UTC 2025 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos1-amd64, called using "1 libbpp-seq unstable /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn 2.4.1-13" as arguments. Tue Sep 16 09:34:55 UTC 2025 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-2n5XKTBp" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Tue Sep 16 09:34:55 UTC 2025 I: Downloading source for unstable/libbpp-seq=2.4.1-13 Reading package lists... NOTICE: 'libbpp-seq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libbpp-seq.git Please use: git clone https://salsa.debian.org/med-team/libbpp-seq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 337 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (dsc) [2169 B] Get:2 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (tar) [323 kB] Get:3 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (diff) [12.2 kB] Fetched 337 kB in 0s (8700 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libbpp-seq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libbpp-seq.git Please use: git clone https://salsa.debian.org/med-team/libbpp-seq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 337 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (dsc) [2169 B] Get:2 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (tar) [323 kB] Get:3 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (diff) [12.2 kB] Fetched 337 kB in 0s (8700 kB/s) Download complete and in download only mode ============================================================================= Building libbpp-seq in unstable on amd64 on ionos1-amd64 now. Date: Tue Sep 16 09:34:56 UTC 2025 Date UTC: Tue Sep 16 09:34:56 UTC 2025 ============================================================================= W: /root/.pbuilderrc does not exist I: Logging to b1/build.log I: pbuilder: network access will be disabled during build I: Current time: Mon Sep 15 21:34:56 -12 2025 I: pbuilder-time-stamp: 1758015296 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbpp-seq_2.4.1-13.dsc] I: copying [./libbpp-seq_2.4.1.orig.tar.gz] I: copying [./libbpp-seq_2.4.1-13.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbpp-seq_2.4.1-13.dsc: 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_2.4.1-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying unforce-cxxflags.patch dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/510047/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='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6d39a27387004a52a7448e70acdd1e81' 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='510047' 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.Ao7rVHRn/pbuilderrc_cOLk --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b1 --logfile b1/build.log libbpp-seq_2.4.1-13.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 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) 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/510047/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 ... 19917 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} 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, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 33.1 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-1 [2268 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-1 [12.0 MB] Get: 48 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 55 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbpp-core4t64 amd64 2.4.1-13+b1 [629 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libbpp-core-dev amd64 2.4.1-13+b1 [967 kB] Fetched 33.1 MB in 0s (144 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... 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. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libbpp-seq-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbpp-seq_2.4.1-13_source.changes dpkg-buildpackage: info: source package libbpp-seq dpkg-buildpackage: info: source version 2.4.1-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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 .. CMake Deprecation Warning at CMakeLists.txt:8 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The CXX compiler identification is GNU 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 (0.3s) -- 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 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/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 -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/build 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[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' [ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o [ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o [ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o [ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o [ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o [ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o [ 3%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o [ 4%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o [ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o [ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o [ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o [ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o [ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g 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/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/AbstractAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.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++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/bpp-seq-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 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/AlphabetExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/CodonAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp 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/BinaryAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp 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/DNA.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 9%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o [ 10%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.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/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp 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 [ 10%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o [ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.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 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/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp [ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o [ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o [ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/DefaultAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp [ 13%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o [ 13%] 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/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o 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 [ 14%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp 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/LetterAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp 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 CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp 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/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 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-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/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 [ 15%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp [ 20%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp 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/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp 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 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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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 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/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp [ 22%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp [ 22%] 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 [ 23%] 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/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 [ 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-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 [ 24%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp [ 25%] 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/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp [ 26%] 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 [ 26%] 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 [ 26%] 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 [ 27%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o [ 28%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 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 [ 29%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 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/SiteContainerExceptions.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 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/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; | ^~~~~~~~ [ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o /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; | ^~~~~~~~ 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/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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/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 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; | ^~~~~~~~ [ 31%] 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 [ 32%] 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 [ 32%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 33%] 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/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: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; | ^~~~~~~~ [ 33%] 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 [ 33%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 34%] 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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-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++ -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; | ^~~~~~~~ [ 35%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.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 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; | ^~~~~~~~ [ 36%] 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 [ 36%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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/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; | ^~~~~~~~ [ 37%] 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++ -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 [ 37%] 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 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; | ^~~~~~~~ [ 38%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 38%] 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 [ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 40%] 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 [ 40%] 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 [ 40%] 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 [ 41%] 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 [ 42%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 [ 42%] 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 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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 43%] 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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-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 [ 44%] 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 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; | ^~~~~~~~ [ 45%] 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/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; | ^~~~~~~~ [ 45%] 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 [ 46%] 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 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; | ^~~~~~~~ [ 46%] 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 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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 47%] 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 [ 48%] 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 [ 48%] 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 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; | ^~~~~~~~ [ 48%] 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 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))); | ^ 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))); | ^ [ 49%] 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 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))); | ^ [ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/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; | ^~~~~~~~ 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 [ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o [ 51%] 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 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 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; | ^~~~~~~~ [ 51%] 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 [ 52%] 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/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))); | ^ 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/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; | ^~~~~~~~ [ 52%] 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 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/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: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; | ^~~~~~~~ [ 53%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 53%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h: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; | ^~~~~~~~ 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 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: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/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; | ^~~~~~~~ [ 53%] 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 [ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 55%] 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 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; | ^~~~~~~~ [ 55%] 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 [ 55%] 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++ -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 [ 56%] 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 [ 57%] 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 [ 57%] 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 [ 57%] 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/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; | ^~~~~~~~ [ 58%] 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 [ 59%] 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 [ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o 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))); | ^ 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 /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))); | ^ 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: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; | ^~~~~~~~ [ 61%] 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 [ 62%] 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/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; | ^~~~~~~~ [ 62%] 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 [ 62%] 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 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; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 63%] 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++ -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 [ 64%] 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 [ 64%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 64%] 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 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; | ^~~~~~~~ [ 64%] 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 [ 65%] 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 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))); | ^ [ 65%] 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/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))); | ^ [ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.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/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 [ 68%] 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/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: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; | ^~~~~~~~ [ 68%] 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/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/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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 69%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 69%] 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/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 [ 69%] 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 [ 70%] 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 [ 71%] 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 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; | ^~~~~~~~ [ 72%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.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 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: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; | ^~~~~~~~ [ 72%] 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 /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, | ^~~~~~ [ 72%] 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 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; | ^~~~~~~~ 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/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: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: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; | ^~~~~~~~ [ 73%] 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 [ 73%] 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 [ 74%] 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 [ 75%] 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 [ 76%] 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/MaseTools.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 76%] 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++ -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 [ 76%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o [ 77%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 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 [ 78%] 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 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; | ^~~~~~~~ [ 78%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 79%] 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 [ 80%] 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 [ 80%] 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 [ 80%] 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 [ 81%] 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 [ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o [ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o [ 83%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o [ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.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 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 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 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 [ 84%] 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 [ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o 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; | ^~~~~~~~ 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 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; | ^~~~~~~~ [ 85%] 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 [ 85%] 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 [ 86%] 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 [ 86%] 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 [ 87%] 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 [ 87%] 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 [ 88%] 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 [ 89%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o [ 89%] 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 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 [ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.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 [ 90%] 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 /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, | ^~~~~~ [ 91%] 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" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o" 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"CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o" "CMakeFiles/bpp-seq-[ 92%] 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" 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"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" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o" /usr/lib/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[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_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_alphabets.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/depend 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_bowker.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_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_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[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/build make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.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 -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/build 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]: 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]: 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 -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[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' 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' [ 93%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o [ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o [ 95%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o [ 96%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.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_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_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 [ 96%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.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_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_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 [ 97%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.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_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_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 [ 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_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 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' [ 98%] Built target bpp-seq-static 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; | ^~~~~~~~ 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: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/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/test/test_io.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 99%] Linking CXX executable test_walker [ 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 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_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 /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_walker.dir/link.d CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 [ 99%] Linking CXX executable test_alphabets make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_sequences.dir/link.d CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /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/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alphabets.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_containers.dir/link.d CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 99%] Built target test_walker [ 99%] Built target test_containers /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alphabets.dir/link.d CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 [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 [100%] 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 /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alignment_scores.dir/link.d CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -o test_alignment_scores -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [100%] Built target test_alignment_scores /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_io.dir/link.d CMakeFiles/test_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [100%] Built target test_io 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 1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 0 1: 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.333333 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.333333 1.000000 1.000000 1.000000 1.000000 3: 2 0.919699 4: 47 4: ----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU-- 4: ---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU-- 4: [>>> ] 8% [>>>> ] 12% [>>>>>> ] 17% [>>>>>>>> ] 21% [>>>>>>>>> ] 25% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 38% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>>>> ] 51% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% 4: 30 4: -AUGCCGGCGUUUUG-G-CCGACGUGUUUU 4: GAAGGCGG-GUUUUGCGACCGACG--UUUU 1/7 Test #1: test_alignment_scores ............ Passed 0.01 sec 2/7 Test #2: test_alphabets ................... Passed 0.01 sec 3/7 Test #4: test_containers .................. Passed 0.01 sec 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 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% 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: _________________________________________________ 7: 0 - 0 7: 1 - 0 7: 2 - 0 7: 3 - 0 7: 4 A 0 7: 5 U 1 7: 6 G 2 7: 7 C 3 7: 8 C 4 7: 9 G 5 7: 10 - 5 7: 11 - 5 7: 12 - 5 7: 13 G 6 7: 14 C 7 7: 15 G 8 7: 16 U 9 7: 17 - 9 7: 18 - 9 7: 19 - 9 7: 20 - 9 7: 21 U 10 7: 22 U 11 7: 23 U 12 7: 24 - 12 7: 25 - 12 7: 26 - 12 7: 27 - 12 7: 28 G 13 7: 29 - 13 7: 30 - 13 7: 31 G 14 7: 32 - 14 7: 33 C 15 7: 34 C 16 7: 35 G 17 7: 36 A 18 7: 37 C 19 7: 38 G 20 7: 39 U 21 7: 40 G 22 7: 41 U 23 7: 42 U 24 7: 43 U 25 7: 44 U 26 7: 45 - 26 7: 46 - 26 7: 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 5/7 Test #7: test_walker ...................... Passed 0.01 sec 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 6/7 Test #5: test_io .......................... Passed 0.03 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%0.0068 0.0448 0.096 0.504 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%0.0102 0.0504 0.1044 0.5098 7/7 Test #3: test_bowker ...................... Passed 15.18 sec 100% tests passed, 0 tests failed out of 7 Total Test time (real) = 15.19 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-seq-dev' in '../libbpp-seq-dev_2.4.1-13_amd64.deb'. dpkg-deb: building package 'libbpp-seq12t64' in '../libbpp-seq12t64_2.4.1-13_amd64.deb'. dpkg-deb: building package 'libbpp-seq12t64-dbgsym' in '../libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-seq_2.4.1-13_amd64.buildinfo dpkg-genchanges --build=binary -O../libbpp-seq_2.4.1-13_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/510047 and its subdirectories I: Current time: Mon Sep 15 21:36:17 -12 2025 I: pbuilder-time-stamp: 1758015377 Tue Sep 16 09:36:17 UTC 2025 I: Signing ./b1/libbpp-seq_2.4.1-13_amd64.buildinfo as libbpp-seq_2.4.1-13_amd64.buildinfo.asc Tue Sep 16 09:36:17 UTC 2025 I: Signed ./b1/libbpp-seq_2.4.1-13_amd64.buildinfo as ./b1/libbpp-seq_2.4.1-13_amd64.buildinfo.asc Tue Sep 16 09:36:17 UTC 2025 - build #1 for libbpp-seq/unstable/amd64 on ionos1-amd64 done. Starting cleanup. All cleanup done. Tue Sep 16 09:36:17 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-2n5XKTBp, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn: total 16 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 09:36 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 09:34 b2 -rw-rw-r-- 1 jenkins jenkins 2169 Aug 7 2024 libbpp-seq_2.4.1-13.dsc -rw------- 1 jenkins jenkins 3298 Sep 16 09:34 rbuildlog.YNoJkpl /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b1: total 11404 -rw-r--r-- 1 jenkins jenkins 372727 Sep 16 09:36 build.log -rw-r--r-- 1 jenkins jenkins 739360 Sep 16 09:36 libbpp-seq-dev_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 9979824 Sep 16 09:36 libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 508980 Sep 16 09:36 libbpp-seq12t64_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 12244 Sep 16 09:36 libbpp-seq_2.4.1-13.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2169 Sep 16 09:36 libbpp-seq_2.4.1-13.dsc -rw-r--r-- 1 jenkins jenkins 6593 Sep 16 09:36 libbpp-seq_2.4.1-13_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7475 Sep 16 09:36 libbpp-seq_2.4.1-13_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1937 Sep 16 09:36 libbpp-seq_2.4.1-13_amd64.changes -rw-r--r-- 1 jenkins jenkins 1415 Sep 16 09:36 libbpp-seq_2.4.1-13_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b2: total 0 Tue Sep 16 09:36:17 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Sep 15 21:34:56 -12 2025 I: pbuilder-time-stamp: 1758015296 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbpp-seq_2.4.1-13.dsc] I: copying [./libbpp-seq_2.4.1.orig.tar.gz] I: copying [./libbpp-seq_2.4.1-13.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbpp-seq_2.4.1-13.dsc: 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_2.4.1-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying unforce-cxxflags.patch dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/510047/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='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='6d39a27387004a52a7448e70acdd1e81' 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='510047' 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.Ao7rVHRn/pbuilderrc_cOLk --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b1 --logfile b1/build.log libbpp-seq_2.4.1-13.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 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) 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/510047/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 ... 19917 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} 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, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 33.1 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-1 [2268 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-1 [12.0 MB] Get: 48 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 55 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbpp-core4t64 amd64 2.4.1-13+b1 [629 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libbpp-core-dev amd64 2.4.1-13+b1 [967 kB] Fetched 33.1 MB in 0s (144 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... 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 ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../18-cmake-data_4.1.1+really3.31.6-1_all.deb ... Unpacking cmake-data (4.1.1+really3.31.6-1) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../19-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../20-libarchive13t64_3.7.4-4+b1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../21-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../22-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../23-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../24-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../25-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../26-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../27-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../28-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../29-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../30-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../31-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../32-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../33-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../34-libnghttp3-9_1.11.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../35-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../36-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../37-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../38-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../39-libgnutls30t64_3.8.10-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../40-librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../41-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../42-libcurl4t64_8.16.0-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.16.0-1) ... Selecting previously unselected package libjsoncpp26:amd64. Preparing to unpack .../43-libjsoncpp26_1.9.6-4_amd64.deb ... Unpacking libjsoncpp26:amd64 (1.9.6-4) ... Selecting previously unselected package librhash1:amd64. 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libbpp-seq-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbpp-seq_2.4.1-13_source.changes dpkg-buildpackage: info: source package libbpp-seq dpkg-buildpackage: info: source version 2.4.1-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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 .. CMake Deprecation Warning at CMakeLists.txt:8 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The CXX compiler identification is GNU 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 (0.3s) -- 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 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/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 -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/build 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[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' [ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o [ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o [ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o [ 1%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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/AbstractAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.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++ -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/AlphabetExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/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 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/AlphabetExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/CodonAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp 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/BinaryAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp 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/DNA.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 9%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o [ 10%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.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/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp 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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src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.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/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp 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 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src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp 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/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 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-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/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 [ 15%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp [ 20%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp 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/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp 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 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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 [ 21%] 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++ -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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ 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-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/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp [ 22%] 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 [ 23%] 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 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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 [ 26%] 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 [ 27%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o [ 28%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 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 [ 29%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 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/SiteContainerExceptions.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 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/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; | ^~~~~~~~ [ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o /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; | ^~~~~~~~ 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/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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/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 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; | ^~~~~~~~ [ 31%] 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 [ 32%] 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 [ 32%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 33%] 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/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: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; | ^~~~~~~~ [ 33%] 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 [ 33%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 34%] 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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-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++ -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; | ^~~~~~~~ [ 35%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.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 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; | ^~~~~~~~ [ 36%] 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 [ 36%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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/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; | ^~~~~~~~ [ 37%] 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++ -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 [ 37%] 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 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; | ^~~~~~~~ [ 38%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 38%] 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 [ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 40%] 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 [ 40%] 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 [ 40%] 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 [ 41%] 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 [ 42%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 [ 42%] 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 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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 43%] 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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-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 [ 44%] 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 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; | ^~~~~~~~ [ 45%] 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/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; | ^~~~~~~~ [ 45%] 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 [ 46%] 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 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; | ^~~~~~~~ [ 46%] 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 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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 47%] 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 [ 48%] 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 [ 48%] 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 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; | ^~~~~~~~ [ 48%] 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 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))); | ^ 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))); | ^ [ 49%] 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 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))); | ^ [ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/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; | ^~~~~~~~ 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 [ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o [ 51%] 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 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 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; | ^~~~~~~~ [ 51%] 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 [ 52%] 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/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))); | ^ 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/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; | ^~~~~~~~ [ 52%] 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 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/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: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; | ^~~~~~~~ [ 53%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 53%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h: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; | ^~~~~~~~ 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 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: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/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; | ^~~~~~~~ [ 53%] 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 [ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 55%] 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 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; | ^~~~~~~~ [ 55%] 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 [ 55%] 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++ -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 [ 56%] 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 [ 57%] 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 [ 57%] 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 [ 57%] 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/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; | ^~~~~~~~ [ 58%] 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 [ 59%] 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 [ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o 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))); | ^ 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 /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))); | ^ 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: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; | ^~~~~~~~ [ 61%] 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 [ 62%] 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/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; | ^~~~~~~~ [ 62%] 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 [ 62%] 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 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; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 63%] 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++ -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 [ 64%] 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 [ 64%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 64%] 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 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; | ^~~~~~~~ [ 64%] 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 [ 65%] 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 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))); | ^ [ 65%] 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/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))); | ^ [ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.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/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 [ 68%] 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/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: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; | ^~~~~~~~ [ 68%] 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/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/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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 69%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 69%] 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/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 [ 69%] 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 [ 70%] 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 [ 71%] 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 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; | ^~~~~~~~ [ 72%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.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 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: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; | ^~~~~~~~ [ 72%] 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 /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, | ^~~~~~ [ 72%] 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 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; | ^~~~~~~~ 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/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: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: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; | ^~~~~~~~ [ 73%] 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 [ 73%] 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 [ 74%] 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 [ 75%] 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 [ 76%] 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/MaseTools.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 76%] 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++ -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 [ 76%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o [ 77%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 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 [ 78%] 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 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; | ^~~~~~~~ [ 78%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 79%] 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 [ 80%] 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 [ 80%] 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 [ 80%] 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 [ 81%] 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 [ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o [ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o [ 83%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o [ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.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 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 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 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 [ 84%] 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 [ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o 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; | ^~~~~~~~ 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 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; | ^~~~~~~~ [ 85%] 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 [ 85%] 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 [ 86%] 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 [ 86%] 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 [ 87%] 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 [ 87%] 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 [ 88%] 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 [ 89%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o [ 89%] 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 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 [ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.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 [ 90%] 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 /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, | ^~~~~~ [ 91%] 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" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o" 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"CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o" "CMakeFiles/bpp-seq-[ 92%] 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" 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"CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o" 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"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[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_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_alphabets.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/depend 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_bowker.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_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_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[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/build make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.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 -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/build 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]: 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]: 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 -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[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' 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' [ 93%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o [ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o [ 95%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o [ 96%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.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_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_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 [ 96%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.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_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_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 [ 97%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.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_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_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 [ 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_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 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' [ 98%] Built target bpp-seq-static 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; | ^~~~~~~~ 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: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/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/test/test_io.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 99%] Linking CXX executable test_walker [ 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 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_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 /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_walker.dir/link.d CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 [ 99%] Linking CXX executable test_alphabets make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_sequences.dir/link.d CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /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/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alphabets.dir/link.txt --verbose=1 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_containers.dir/link.d CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 99%] Built target test_walker [ 99%] Built target test_containers /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alphabets.dir/link.d CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 [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 [100%] 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 /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alignment_scores.dir/link.d CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -o test_alignment_scores -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [100%] Built target test_alignment_scores /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_io.dir/link.d CMakeFiles/test_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [100%] Built target test_io 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 1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 0 1: 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.333333 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.333333 1.000000 1.000000 1.000000 1.000000 3: 2 0.919699 4: 47 4: ----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU-- 4: ---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU-- 4: [>>> ] 8% [>>>> ] 12% [>>>>>> ] 17% [>>>>>>>> ] 21% [>>>>>>>>> ] 25% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 38% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>>>> ] 51% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% 4: 30 4: -AUGCCGGCGUUUUG-G-CCGACGUGUUUU 4: GAAGGCGG-GUUUUGCGACCGACG--UUUU 1/7 Test #1: test_alignment_scores ............ Passed 0.01 sec 2/7 Test #2: test_alphabets ................... Passed 0.01 sec 3/7 Test #4: test_containers .................. Passed 0.01 sec 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 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% 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: _________________________________________________ 7: 0 - 0 7: 1 - 0 7: 2 - 0 7: 3 - 0 7: 4 A 0 7: 5 U 1 7: 6 G 2 7: 7 C 3 7: 8 C 4 7: 9 G 5 7: 10 - 5 7: 11 - 5 7: 12 - 5 7: 13 G 6 7: 14 C 7 7: 15 G 8 7: 16 U 9 7: 17 - 9 7: 18 - 9 7: 19 - 9 7: 20 - 9 7: 21 U 10 7: 22 U 11 7: 23 U 12 7: 24 - 12 7: 25 - 12 7: 26 - 12 7: 27 - 12 7: 28 G 13 7: 29 - 13 7: 30 - 13 7: 31 G 14 7: 32 - 14 7: 33 C 15 7: 34 C 16 7: 35 G 17 7: 36 A 18 7: 37 C 19 7: 38 G 20 7: 39 U 21 7: 40 G 22 7: 41 U 23 7: 42 U 24 7: 43 U 25 7: 44 U 26 7: 45 - 26 7: 46 - 26 7: 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 5/7 Test #7: test_walker ...................... Passed 0.01 sec 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 6/7 Test #5: test_io .......................... Passed 0.03 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%0.0068 0.0448 0.096 0.504 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%0.0102 0.0504 0.1044 0.5098 7/7 Test #3: test_bowker ...................... Passed 15.18 sec 100% tests passed, 0 tests failed out of 7 Total Test time (real) = 15.19 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-seq-dev' in '../libbpp-seq-dev_2.4.1-13_amd64.deb'. dpkg-deb: building package 'libbpp-seq12t64' in '../libbpp-seq12t64_2.4.1-13_amd64.deb'. dpkg-deb: building package 'libbpp-seq12t64-dbgsym' in '../libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-seq_2.4.1-13_amd64.buildinfo dpkg-genchanges --build=binary -O../libbpp-seq_2.4.1-13_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/510047 and its subdirectories I: Current time: Mon Sep 15 21:36:17 -12 2025 I: pbuilder-time-stamp: 1758015377 Tue Sep 16 09:36:18 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Tue Sep 16 09:36:18 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Tue Sep 16 09:36:18 UTC 2025 - checking /var/lib/jenkins/offline_nodes if ionos15-amd64.debian.net is marked as down. Tue Sep 16 09:36:18 UTC 2025 - checking via ssh if ionos15-amd64.debian.net is up. removed '/tmp/read-only-fs-test-DuVG9e' ==================================================================================== Mon Oct 19 15:59:18 UTC 2026 - running /srv/jenkins/bin/reproducible_build.sh (for job /srv/jenkins/bin/reproducible_build.sh) on ionos15-amd64, called using "2 libbpp-seq unstable /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn 2.4.1-13" as arguments. Mon Oct 19 15:59:18 UTC 2026 - actually running "reproducible_build.sh" (md5sum cc591790ab2c8e13f5e554202b95c89c) as "/tmp/jenkins-script-Cj3ZXEmO" $ git clone https://salsa.debian.org/qa/jenkins.debian.net.git ; more CONTRIBUTING Mon Oct 19 15:59:18 UTC 2026 I: Downloading source for unstable/libbpp-seq=2.4.1-13 Reading package lists... NOTICE: 'libbpp-seq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libbpp-seq.git Please use: git clone https://salsa.debian.org/med-team/libbpp-seq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 337 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (dsc) [2169 B] Get:2 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (tar) [323 kB] Get:3 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (diff) [12.2 kB] Fetched 337 kB in 0s (2219 kB/s) Download complete and in download only mode Reading package lists... NOTICE: 'libbpp-seq' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/libbpp-seq.git Please use: git clone https://salsa.debian.org/med-team/libbpp-seq.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 337 kB of source archives. Get:1 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (dsc) [2169 B] Get:2 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (tar) [323 kB] Get:3 http://deb.debian.org/debian unstable/main libbpp-seq 2.4.1-13 (diff) [12.2 kB] Fetched 337 kB in 0s (2219 kB/s) Download complete and in download only mode ============================================================================= Re-Building libbpp-seq in unstable on amd64 on ionos15-amd64 now. Date: Mon Oct 19 15:59:18 UTC 2026 Date UTC: Mon Oct 19 15:59:18 UTC 2026 ============================================================================= ++ mktemp -t pbuilderrc_XXXX --tmpdir=/srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn + local TMPCFG=/srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/pbuilderrc_PF9L + case ${ARCH} in + case $ARCH in + locale=et_EE + language=et + case "${SUITE}" in + reproducible_buildflags=+all + extra_deb_build_options= + case "${SRCPACKAGE}" in + cat + echo BUILDDIR=/build/reproducible-path + '[' libbpp-seq = debian-installer -o libbpp-seq = debian-installer-netboot-images ']' + pbuilder_options=() + local pbuilder_options + DEBBUILDOPTS=-b + BINARYTARGET= + '[' libbpp-seq = u-boot ']' + case "${SRCPACKAGE}" in + PBUILDERTIMEOUT=24 + local PRESULT=0 + sudo timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/pbuilderrc_PF9L --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b2 --logfile b2/build.log libbpp-seq_2.4.1-13.dsc W: /root/.pbuilderrc does not exist I: Logging to b2/build.log I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 20 05:59:19 +14 2026 I: pbuilder-time-stamp: 1792425559 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [libbpp-seq_2.4.1-13.dsc] I: copying [./libbpp-seq_2.4.1.orig.tar.gz] I: copying [./libbpp-seq_2.4.1-13.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbpp-seq_2.4.1-13.dsc: 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_2.4.1-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying unforce-cxxflags.patch dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/550582/tmp/hooks/D01_modify_environment starting debug: Running on ionos15-amd64. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash '/bin/sh' -> '/bin/bash' lrwxrwxrwx 1 root root 9 Oct 19 15:59 /bin/sh -> /bin/bash I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/550582/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/550582/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") BASH_VERSION='5.3.3(1)-release' BUILDDIR=/build/reproducible-path BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=amd64 DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' DIRSTACK=() DISTRIBUTION=unstable EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=x86_64 HOST_ARCH=amd64 IFS=' ' INVOCATION_ID=0f62d4af0fa44f76ad4a390a78600d41 LANG=C LANGUAGE=et_EE:et LC_ALL=C MACHTYPE=x86_64-pc-linux-gnu MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnu PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=550582 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/pbuilderrc_PF9L --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b2 --logfile b2/build.log libbpp-seq_2.4.1-13.dsc' SUDO_GID=111 SUDO_HOME=/var/lib/jenkins SUDO_UID=106 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://213.165.73.152:3128 I: uname -a Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin I: user script /srv/workspace/pbuilder/550582/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 ... 19917 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} 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, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 33.1 MB of archives. After unpacking 126 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.7.1-2 [108 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-3 [100 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get: 15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 cmake-data all 4.1.1+really3.31.6-1 [2268 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 27 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-9 [19.8 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-9 [57.5 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.11.0-1 [73.7 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libgnutls30t64 amd64 3.8.10-2 [1484 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.16.0-1 [437 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 cmake amd64 4.1.1+really3.31.6-1 [12.0 MB] Get: 48 http://deb.debian.org/debian unstable/main amd64 d-shlibs all 0.109 [11.1 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 54 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 55 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbpp-core4t64 amd64 2.4.1-13+b1 [629 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libbpp-core-dev amd64 2.4.1-13+b1 [967 kB] Fetched 33.1 MB in 0s (129 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 ... 19917 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.1-2_amd64.deb ... Unpacking libexpat1:amd64 (2.7.1-2) ... 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 ... Unpacking libuchardet0:amd64 (0.0.8-2) ... Selecting previously unselected package groff-base. Preparing to unpack .../09-groff-base_1.23.0-9_amd64.deb ... Unpacking groff-base (1.23.0-9) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../10-bsdextrautils_2.41.1-3_amd64.deb ... Unpacking bsdextrautils (2.41.1-3) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../11-libpipeline1_1.5.8-1_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../12-man-db_2.13.1-1_amd64.deb ... Unpacking man-db (2.13.1-1) ... Selecting previously unselected package m4. Preparing to unpack .../13-m4_1.4.20-1_amd64.deb ... Unpacking m4 (1.4.20-1) ... Selecting previously unselected package autoconf. Preparing to unpack .../14-autoconf_2.72-3.1_all.deb ... Unpacking autoconf (2.72-3.1) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../15-autotools-dev_20240727.1_all.deb ... Unpacking autotools-dev (20240727.1) ... Selecting previously unselected package automake. Preparing to unpack .../16-automake_1%3a1.17-4_all.deb ... Unpacking automake (1:1.17-4) ... Selecting previously unselected package autopoint. Preparing to unpack .../17-autopoint_0.23.1-2_all.deb ... Unpacking autopoint (0.23.1-2) ... Selecting previously unselected package cmake-data. Preparing to unpack .../18-cmake-data_4.1.1+really3.31.6-1_all.deb ... Unpacking cmake-data (4.1.1+really3.31.6-1) ... Selecting previously unselected package libxml2-16:amd64. Preparing to unpack .../19-libxml2-16_2.14.5+dfsg-0.2_amd64.deb ... Unpacking libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Selecting previously unselected package libarchive13t64:amd64. Preparing to unpack .../20-libarchive13t64_3.7.4-4+b1_amd64.deb ... Unpacking libarchive13t64:amd64 (3.7.4-4+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../21-libbrotli1_1.1.0-2+b7_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b7) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../22-libkrb5support0_1.21.3-5_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-5) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../23-libcom-err2_1.47.2-3+b3_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-3+b3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../24-libk5crypto3_1.21.3-5_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../25-libkeyutils1_1.6.3-6_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-6) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../26-libkrb5-3_1.21.3-5_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-5) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../27-libgssapi-krb5-2_1.21.3-5_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-5) ... Selecting previously unselected package libunistring5:amd64. Preparing to unpack .../28-libunistring5_1.3-2_amd64.deb ... Unpacking libunistring5:amd64 (1.3-2) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../29-libidn2-0_2.3.8-4_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.8-4) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../30-libsasl2-modules-db_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../31-libsasl2-2_2.1.28+dfsg1-9_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Selecting previously unselected package libldap2:amd64. Preparing to unpack .../32-libldap2_2.6.10+dfsg-1_amd64.deb ... Unpacking libldap2:amd64 (2.6.10+dfsg-1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../33-libnghttp2-14_1.64.0-1.1+b1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../34-libnghttp3-9_1.11.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.11.0-1) ... Selecting previously unselected package libpsl5t64:amd64. Preparing to unpack .../35-libpsl5t64_0.21.2-1.1+b1_amd64.deb ... Unpacking libpsl5t64:amd64 (0.21.2-1.1+b1) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../36-libffi8_3.5.2-2_amd64.deb ... Unpacking libffi8:amd64 (3.5.2-2) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../37-libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../38-libtasn1-6_4.20.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.20.0-2) ... Selecting previously unselected package libgnutls30t64:amd64. Preparing to unpack .../39-libgnutls30t64_3.8.10-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.10-2) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../40-librtmp1_2.4+20151223.gitfa8646d.1-3_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../41-libssh2-1t64_1.11.1-1_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../42-libcurl4t64_8.16.0-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.16.0-1) ... Selecting previously unselected package libjsoncpp26:amd64. Preparing to unpack .../43-libjsoncpp26_1.9.6-4_amd64.deb ... Unpacking libjsoncpp26:amd64 (1.9.6-4) ... Selecting previously unselected package librhash1:amd64. Preparing to unpack .../44-librhash1_1.4.6-1_amd64.deb ... Unpacking librhash1:amd64 (1.4.6-1) ... Selecting previously unselected package libuv1t64:amd64. Preparing to unpack .../45-libuv1t64_1.51.0-2_amd64.deb ... Unpacking libuv1t64:amd64 (1.51.0-2) ... Selecting previously unselected package cmake. Preparing to unpack .../46-cmake_4.1.1+really3.31.6-1_amd64.deb ... Unpacking cmake (4.1.1+really3.31.6-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../47-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../48-libdebhelper-perl_13.26_all.deb ... Unpacking libdebhelper-perl (13.26) ... Selecting previously unselected package libtool. Preparing to unpack .../49-libtool_2.5.4-5_all.deb ... Unpacking libtool (2.5.4-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../50-dh-autoreconf_21_all.deb ... Unpacking dh-autoreconf (21) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../51-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../52-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../53-dh-strip-nondeterminism_1.15.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.15.0-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../54-libelf1t64_0.193-3_amd64.deb ... Unpacking libelf1t64:amd64 (0.193-3) ... Selecting previously unselected package dwz. Preparing to unpack .../55-dwz_0.16-2_amd64.deb ... Unpacking dwz (0.16-2) ... Selecting previously unselected package gettext. Preparing to unpack .../56-gettext_0.23.1-2+b1_amd64.deb ... Unpacking gettext (0.23.1-2+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../57-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../58-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../59-debhelper_13.26_all.deb ... Unpacking debhelper (13.26) ... Selecting previously unselected package libbpp-core4t64:amd64. Preparing to unpack .../60-libbpp-core4t64_2.4.1-13+b1_amd64.deb ... Unpacking libbpp-core4t64:amd64 (2.4.1-13+b1) ... Selecting previously unselected package libbpp-core-dev:amd64. Preparing to unpack .../61-libbpp-core-dev_2.4.1-13+b1_amd64.deb ... Unpacking libbpp-core-dev:amd64 (2.4.1-13+b1) ... Setting up libexpat1:amd64 (2.7.1-2) ... Setting up libpipeline1:amd64 (1.5.8-1) ... Setting up libkeyutils1:amd64 (1.6.3-6) ... Setting up bsdextrautils (2.41.1-3) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libbpp-core4t64:amd64 (2.4.1-13+b1) ... Setting up libdebhelper-perl (13.26) ... Setting up libbrotli1:amd64 (1.1.0-2+b7) ... Setting up libuv1t64:amd64 (1.51.0-2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up libcom-err2:amd64 (1.47.2-3+b3) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-3) ... Setting up libkrb5support0:amd64 (1.21.3-5) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Setting up libbpp-core-dev:amd64 (2.4.1-13+b1) ... Setting up autotools-dev (20240727.1) ... Setting up libjsoncpp26:amd64 (1.9.6-4) ... Setting up libproc2-0:amd64 (2:4.0.4-9) ... Setting up libunistring5:amd64 (1.3-2) ... Setting up autopoint (0.23.1-2) ... Setting up d-shlibs (0.109) ... Setting up libk5crypto3:amd64 (1.21.3-5) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Setting up autoconf (2.72-3.1) ... Setting up libnghttp3-9:amd64 (1.11.0-1) ... Setting up libffi8:amd64 (3.5.2-2) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up procps (2:4.0.4-9) ... Setting up libtasn1-6:amd64 (4.20.0-2) ... Setting up cmake-data (4.1.1+really3.31.6-1) ... Setting up librhash1:amd64 (1.4.6-1) ... Setting up libkrb5-3:amd64 (1.21.3-5) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libarchive13t64:amd64 (3.7.4-4+b1) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.15.0-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (21) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-9) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up po-debconf (1.0.21+nmu1) ... 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 (8.16.0-1) ... Setting up debhelper (13.26) ... Setting up cmake (4.1.1+really3.31.6-1) ... 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 I: Building the package I: user script /srv/workspace/pbuilder/550582/tmp/hooks/A99_set_merged_usr starting Not re-configuring usrmerge for unstable I: user script /srv/workspace/pbuilder/550582/tmp/hooks/A99_set_merged_usr finished hostname: Name or service not known I: Running cd /build/reproducible-path/libbpp-seq-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbpp-seq_2.4.1-13_source.changes dpkg-buildpackage: info: source package libbpp-seq dpkg-buildpackage: info: source version 2.4.1-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture 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 .. CMake Deprecation Warning at CMakeLists.txt:8 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The CXX compiler identification is GNU 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 (0.3s) -- 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 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/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-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/build make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o [ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o [ 2%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/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 [ 2%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.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 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/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.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/AbstractAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp [ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o [ 3%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o [ 5%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o [ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o [ 5%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o [ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o [ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o [ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp [ 8%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o [ 8%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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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/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 -I/build/reproducible-path/libbpp-seq-2.4.1/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/DNA.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 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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/DNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp 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 [ 12%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o [ 12%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o [ 12%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o [ 12%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/LexicalAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp [ 12%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 /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/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 [ 13%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/ProteicAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp 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++ 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/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNA.cpp [ 14%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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/DefaultAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp 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/RNY.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp [ 16%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o [ 16%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp [ 17%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o [ 17%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o [ 17%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o [ 17%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o [ 18%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o [ 18%] 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/AlphabetIndex/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp [ 20%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o [ 20%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/AAIndex1Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp [ 21%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o 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/AlphabetIndex/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp 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 CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp 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/GranthamAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp [ 21%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp [ 21%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 21%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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/ProteicAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp 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/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++ -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 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/RNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNA.cpp 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 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++ -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 [ 22%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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 /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp [ 23%] 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 [ 23%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp 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; | ^~~~~~~~ [ 24%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp [ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp [ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 25%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 26%] 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 [ 27%] 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++ -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 [ 27%] 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 [ 27%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 28%] 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++ -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 [ 29%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o [ 29%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 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 [ 29%] 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 [ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o [ 30%] 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 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 [ 31%] 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 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; | ^~~~~~~~ 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/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/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/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 31%] 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 [ 32%] 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 [ 33%] 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 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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 34%] 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 [ 34%] 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 [ 35%] 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 [ 35%] 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 [ 36%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 [ 37%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o [ 37%] 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/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 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 [ 37%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 38%] 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 [ 39%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o [ 39%] 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 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 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: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; | ^~~~~~~~ [ 39%] 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++ -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 [ 40%] 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 [ 41%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o [ 41%] 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 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 [ 42%] 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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: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; | ^~~~~~~~ [ 43%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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/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; | ^~~~~~~~ [ 43%] 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/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; | ^~~~~~~~ [ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 44%] 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 [ 45%] 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/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 45%] 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 [ 45%] 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: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; | ^~~~~~~~ [ 46%] 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 47%] 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++ -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/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; | ^~~~~~~~ [ 47%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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; | ^~~~~~~~ [ 47%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.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 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))); | ^ [ 48%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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))); | ^ 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 /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; | ^~~~~~~~ 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))); | ^ [ 49%] 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/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))); | ^ [ 49%] 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 [ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 50%] 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 [ 51%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 51%] 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 [ 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 [ 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/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: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: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-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 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; | ^~~~~~~~ [ 54%] 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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-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 [ 55%] 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 [ 55%] 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/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))); | ^ 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))); | ^ [ 56%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 56%] 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 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))); | ^ [ 56%] 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 [ 57%] 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 [ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/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; | ^~~~~~~~ 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 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/../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; | ^~~~~~~~ [ 59%] 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 [ 59%] 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/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; | ^~~~~~~~ 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/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/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: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; | ^~~~~~~~ [ 60%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o [ 61%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o [ 61%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o [ 62%] 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/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 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 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 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 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:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 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 [ 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 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; | ^~~~~~~~ [ 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 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/../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; | ^~~~~~~~ [ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o [ 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 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 [ 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 65%] 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++ -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 [ 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 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: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; | ^~~~~~~~ [ 66%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 [ 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 [ 67%] 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 [ 67%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o [ 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++ -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 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 [ 69%] 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 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; | ^~~~~~~~ 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; | ^~~~~~~~ [ 69%] 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 [ 70%] 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-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 [ 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: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; | ^~~~~~~~ [ 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/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; | ^~~~~~~~ [ 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/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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/MaseTools.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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/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; | ^~~~~~~~ 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: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; | ^~~~~~~~ [ 74%] 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 [ 74%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.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/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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 74%] 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 [ 75%] 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 [ 76%] 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 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; | ^~~~~~~~ [ 76%] 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 [ 77%] 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 [ 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-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 [ 80%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.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/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 [ 80%] 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/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 [ 80%] 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 [ 81%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o [ 82%] Building CXX object src/CMakeFiles/bpp-seq-static.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/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 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 [ 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 [ 83%] 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 [ 83%] 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 /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, | ^~~~~~ [ 84%] 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 [ 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-shared.dir/Bpp/Seq/SymbolListTools.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 [ 87%] 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 [ 88%] 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-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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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-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 [ 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 /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, | ^~~~~~ [ 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" 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"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" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o" 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"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" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o" 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"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' 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=" 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 -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_bowker.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_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_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[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[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.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 -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_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' 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 -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [ 93%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o [ 93%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.cpp.o [ 94%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.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_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_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 [ 97%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o [ 97%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o [ 97%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o [ 98%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.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_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 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_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_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 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; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/test/test_containers.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/test/test_io.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ [ 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 [ 98%] 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 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' [ 99%] Linking CXX executable test_alphabets [ 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 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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_containers.dir/link.d CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_sequences.dir/link.d CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [ 99%] Built target test_sequences [ 99%] Built target test_containers [ 99%] Built target bpp-seq-static [ 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 [ 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 /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_walker.dir/link.d CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alphabets.dir/link.d CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 [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 [100%] Built target test_alphabets /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [100%] Built target test_bowker /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_io.dir/link.d CMakeFiles/test_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [100%] Built target test_io /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alignment_scores.dir/link.d CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -o test_alignment_scores -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [100%] Built target test_alignment_scores 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 -j42 test ARGS\+=--verbose ARGS\+=-j42 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 -j42 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 1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 0 1: 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.333333 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.333333 1.000000 1.000000 1.000000 1.000000 3: 2 0.919699 4: 47 4: ----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU-- 4: ---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU-- 4: [>>> ] 8% [>>>> ] 12% [>>>>>> ] 17% [>>>>>>>> ] 21% [>>>>>>>>> ] 25% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 38% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>>>> ] 51% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% 4: 30 4: -AUGCCGGCGUUUUG-G-CCGACGUGUUUU 4: GAAGGCGG-GUUUUGCGACCGACG--UUUU 1/7 Test #1: test_alignment_scores ............ Passed 0.01 sec 2/7 Test #2: test_alphabets ................... Passed 0.01 sec 3/7 Test #4: test_containers .................. Passed 0.01 sec 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 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% 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: _________________________________________________ 7: 0 - 0 7: 1 - 0 7: 2 - 0 7: 3 - 0 7: 4 A 0 7: 5 U 1 7: 6 G 2 7: 7 C 3 7: 8 C 4 7: 9 G 5 7: 10 - 5 7: 11 - 5 7: 12 - 5 7: 13 G 6 7: 14 C 7 7: 15 G 8 7: 16 U 9 7: 17 - 9 7: 18 - 9 7: 19 - 9 7: 20 - 9 7: 21 U 10 7: 22 U 11 7: 23 U 12 7: 24 - 12 7: 25 - 12 7: 26 - 12 7: 27 - 12 7: 28 G 13 7: 29 - 13 7: 30 - 13 7: 31 G 14 7: 32 - 14 7: 33 C 15 7: 34 C 16 7: 35 G 17 7: 36 A 18 7: 37 C 19 7: 38 G 20 7: 39 U 21 7: 40 G 22 7: 41 U 23 7: 42 U 24 7: 43 U 25 7: 44 U 26 7: 45 - 26 7: 46 - 26 7: 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 5/7 Test #7: test_walker ...................... Passed 0.01 sec 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 6/7 Test #5: test_io .......................... Passed 0.03 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%0.01 0.049 0.0956 0.5016 3: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0096 0.0486 0.0986 0.5116 7/7 Test #3: test_bowker ...................... Passed 15.16 sec 100% tests passed, 0 tests failed out of 7 Total Test time (real) = 15.16 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 -j42 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/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/SequenceWithQuality.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotationTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex -- 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/AAVolumeIndex.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/AAChargeIndex.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/AASEASup30Index.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/AAIndex1Entry.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEA1030Index.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAMassIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex1.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/GranthamAAChemicalDistance.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/SimpleScore.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/KleinAANetChargeIndex.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/AAChouFasmanAHelixIndex.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/UserAlphabetIndex1.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/AASurfaceIndex.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/SimpleIndexDistance.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/AlignedSequenceContainer.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/CompressedVectorSiteContainer.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/SiteContainerExceptions.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/SiteContainerTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerIterator.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainer.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/VectorSequenceContainer.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/SequenceContainer.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/AbstractSequenceContainer.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/Transliterator.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/AlphabetState.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/DNA.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LexicalAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetNumericState.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/AlphabetExceptions.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/Alphabet.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/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/CodonAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LetterAlphabet.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/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/ProteicAlphabetState.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/WordAlphabet.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/DistanceMatrix.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/CoreSite.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/SiteTools.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/InvertebrateMitochondrialGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/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/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/MoldMitochondrialGeneticCode.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/SequenceWithQualityTools.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/SequenceExceptions.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/SequenceWalker.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/CodonSiteTools.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/SiteExceptions.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/SymbolList.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/SequenceTools.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/Fasta.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Dcse.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/PhredPhd.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/OSequenceStream.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/MaseTools.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/NexusIoSequence.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/Stockholm.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/BppOSequenceStreamReaderFormat.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/BppOAlignmentReaderFormat.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/AbstractIAlignment.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/BppOSequenceWriterFormat.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/SequenceFileIndex.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/StreamSequenceIterator.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/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/BppOAlignmentWriterFormat.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/BppOAlphabetIndex2Format.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex1Format.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractISequence.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/Phylip.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/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-seq-dev' in '../libbpp-seq-dev_2.4.1-13_amd64.deb'. dpkg-deb: building package 'libbpp-seq12t64' in '../libbpp-seq12t64_2.4.1-13_amd64.deb'. dpkg-deb: building package 'libbpp-seq12t64-dbgsym' in '../libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-seq_2.4.1-13_amd64.buildinfo dpkg-genchanges --build=binary -O../libbpp-seq_2.4.1-13_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: user script /srv/workspace/pbuilder/550582/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/550582/tmp/hooks/B01_cleanup finished 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/550582 and its subdirectories I: Current time: Tue Oct 20 06:00:36 +14 2026 I: pbuilder-time-stamp: 1792425636 + false + set +x Mon Oct 19 16:00:36 UTC 2026 I: Signing ./b2/libbpp-seq_2.4.1-13_amd64.buildinfo as libbpp-seq_2.4.1-13_amd64.buildinfo.asc Mon Oct 19 16:00:36 UTC 2026 I: Signed ./b2/libbpp-seq_2.4.1-13_amd64.buildinfo as ./b2/libbpp-seq_2.4.1-13_amd64.buildinfo.asc Mon Oct 19 16:00:36 UTC 2026 - build #2 for libbpp-seq/unstable/amd64 on ionos15-amd64 done. Starting cleanup. All cleanup done. Mon Oct 19 16:00:36 UTC 2026 - reproducible_build.sh stopped running as /tmp/jenkins-script-Cj3ZXEmO, removing. /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn: total 384 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 09:36 b1 drwxrwxr-x 2 jenkins jenkins 4096 Sep 16 09:37 b2 -rw-rw-r-- 1 jenkins jenkins 2169 Aug 7 2024 libbpp-seq_2.4.1-13.dsc -rw------- 1 jenkins jenkins 376313 Sep 16 09:36 rbuildlog.YNoJkpl /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b1: total 11404 -rw-r--r-- 1 jenkins jenkins 372727 Sep 16 09:36 build.log -rw-r--r-- 1 jenkins jenkins 739360 Sep 16 09:36 libbpp-seq-dev_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 9979824 Sep 16 09:36 libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 508980 Sep 16 09:36 libbpp-seq12t64_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 12244 Sep 16 09:36 libbpp-seq_2.4.1-13.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2169 Sep 16 09:36 libbpp-seq_2.4.1-13.dsc -rw-r--r-- 1 jenkins jenkins 6593 Sep 16 09:36 libbpp-seq_2.4.1-13_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7475 Sep 16 09:36 libbpp-seq_2.4.1-13_amd64.buildinfo.asc -rw-r--r-- 1 jenkins jenkins 1937 Sep 16 09:36 libbpp-seq_2.4.1-13_amd64.changes -rw-r--r-- 1 jenkins jenkins 1415 Sep 16 09:36 libbpp-seq_2.4.1-13_source.changes /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b2: total 11404 -rw-rw-r-- 1 jenkins jenkins 374651 Sep 16 09:37 build.log -rw-r--r-- 1 jenkins jenkins 739360 Sep 16 09:37 libbpp-seq-dev_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 9979824 Sep 16 09:37 libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 508980 Sep 16 09:37 libbpp-seq12t64_2.4.1-13_amd64.deb -rw-r--r-- 1 jenkins jenkins 12244 Sep 16 09:37 libbpp-seq_2.4.1-13.debian.tar.xz -rw-r--r-- 1 jenkins jenkins 2169 Sep 16 09:37 libbpp-seq_2.4.1-13.dsc -rw-rw-r-- 1 jenkins jenkins 6593 Sep 16 09:37 libbpp-seq_2.4.1-13_amd64.buildinfo -rw-rw-r-- 1 jenkins jenkins 7475 Sep 16 09:37 libbpp-seq_2.4.1-13_amd64.buildinfo.asc -rw-rw-r-- 1 jenkins jenkins 1937 Sep 16 09:37 libbpp-seq_2.4.1-13_amd64.changes -rw-rw-r-- 1 jenkins jenkins 1415 Sep 16 09:37 libbpp-seq_2.4.1-13_source.changes Tue Sep 16 09:37:37 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Tue Sep 16 09:37:37 UTC 2025 I: libbpp-seq_2.4.1-13_amd64.changes: Format: 1.8 Date: Wed, 07 Aug 2024 10:57:57 +0200 Source: libbpp-seq Binary: libbpp-seq-dev libbpp-seq12t64 libbpp-seq12t64-dbgsym Architecture: amd64 Version: 2.4.1-13 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-seq-dev - Bio++ Sequence library development files libbpp-seq12t64 - Bio++ Sequence library Closes: 1075153 Changes: libbpp-seq (2.4.1-13) unstable; urgency=medium . * Since every GCC version bump ends up in a bug caused by the need to update symbols files we stop providing symbols for this library Closes: #1075153 * lintian-override for no-symbols-control-file Checksums-Sha1: da0de80055987d97e73368b7038af510a254b043 739360 libbpp-seq-dev_2.4.1-13_amd64.deb 30c2f399965a706840e6c8b3084cf4f7ff85d891 9979824 libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb 19f9ccfc2f36416cf5b73a180cf3b00033c397f6 508980 libbpp-seq12t64_2.4.1-13_amd64.deb 4f781a5ff81ccad137c132a3483624683fe7ac3b 6593 libbpp-seq_2.4.1-13_amd64.buildinfo Checksums-Sha256: 86d0dfd8c13dda71212a45cc2fdb94172ef5c3a58ee0f7a15fdf98ed4b6242aa 739360 libbpp-seq-dev_2.4.1-13_amd64.deb bfa104b1468ada04a98cbb98841ab820d4e14ec8681e8346268627348c34ff21 9979824 libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb 6aceb427e8b25da787ee7614d9c9c3ded7d389bcd3e1b3f29e8c2103326316d2 508980 libbpp-seq12t64_2.4.1-13_amd64.deb 307fe6e18054f9ae39c14a1beef4bc199c1be553d0e6cb7ea92aad1010f6e9cd 6593 libbpp-seq_2.4.1-13_amd64.buildinfo Files: 0a3ba2060c8550599bc4eb097e434cd6 739360 libdevel optional libbpp-seq-dev_2.4.1-13_amd64.deb 4d1f26f472132c0a6afa47acb9951a72 9979824 debug optional libbpp-seq12t64-dbgsym_2.4.1-13_amd64.deb e90abe681a7b5dbb8a2115dc024fc78b 508980 libs optional libbpp-seq12t64_2.4.1-13_amd64.deb bac8794e11e04f0c4ace77436f85f253 6593 science optional libbpp-seq_2.4.1-13_amd64.buildinfo removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/libbpp-seq_2.4.1-13.rbuild.log' removed '/var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/libbpp-seq_2.4.1-13.rbuild.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/libbpp-seq_2.4.1-13.build1.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/logs/unstable/amd64/libbpp-seq_2.4.1-13.build2.log.gz' removed '/var/lib/jenkins/userContent/reproducible/debian/buildinfo/unstable/amd64/libbpp-seq_2.4.1-13_amd64.buildinfo' removed '/var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/libbpp-seq_2.4.1-13.diff.gz' Diff of the two buildlogs: -- --- b1/build.log 2025-09-16 09:36:17.497430168 +0000 +++ b2/build.log 2025-09-16 09:37:37.153529396 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Sep 15 21:34:56 -12 2025 -I: pbuilder-time-stamp: 1758015296 +I: Current time: Tue Oct 20 05:59:19 +14 2026 +I: pbuilder-time-stamp: 1792425559 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -25,53 +25,85 @@ dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/510047/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/550582/tmp/hooks/D01_modify_environment starting +debug: Running on ionos15-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Oct 19 15:59 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/550582/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/550582/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='unstable' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="3" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.3.3(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=42 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='6d39a27387004a52a7448e70acdd1e81' - 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='510047' - PS1='# ' - PS2='> ' + INVOCATION_ID=0f62d4af0fa44f76ad4a390a78600d41 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=550582 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.Ao7rVHRn/pbuilderrc_cOLk --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b1 --logfile b1/build.log libbpp-seq_2.4.1-13.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' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/pbuilderrc_PF9L --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b2 --logfile b2/build.log libbpp-seq_2.4.1-13.dsc' + SUDO_GID=111 + SUDO_HOME=/var/lib/jenkins + SUDO_UID=106 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos1-amd64 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.12.43+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.43-1 (2025-08-27) 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/510047/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 10 2025 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/550582/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -175,7 +207,7 @@ Get: 60 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libbpp-core4t64 amd64 2.4.1-13+b1 [629 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libbpp-core-dev amd64 2.4.1-13+b1 [967 kB] -Fetched 33.1 MB in 0s (144 MB/s) +Fetched 33.1 MB in 0s (129 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 ... 19917 files and directories currently installed.) @@ -438,7 +470,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/libbpp-seq-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../libbpp-seq_2.4.1-13_source.changes +I: user script /srv/workspace/pbuilder/550582/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/550582/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/libbpp-seq-2.4.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../libbpp-seq_2.4.1-13_source.changes dpkg-buildpackage: info: source package libbpp-seq dpkg-buildpackage: info: source version 2.4.1-13 dpkg-buildpackage: info: source distribution unstable @@ -486,7 +522,7 @@ -- 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 + cd obj-x86_64-linux-gnu && make -j42 "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 @@ -499,136 +535,177 @@ 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 -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/build make[3]: Leaving 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/build make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' -[ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -[ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -[ 3%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -[ 4%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -[ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o +[ 0%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o +[ 1%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 7%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -[ 8%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -[ 8%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -[ 7%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/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 +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.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/AlphabetExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp +[ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o +[ 3%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o +[ 5%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o +[ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o +[ 5%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o +[ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o +[ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o +[ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp +[ 8%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o +[ 8%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetTools.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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-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/BinaryAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp +[ 10%] 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/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 -[ 9%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -[ 10%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.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 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&& /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/RNY.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp +[ 16%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o +[ 16%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/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/Alphabet/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o 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 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src/CMakeFiles/bpp-seq-static.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/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 -[ 16%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -[ 17%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o +[ 21%] Building CXX object 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-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 +[ 22%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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 /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.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/RNY.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp +[ 23%] 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 +[ 23%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp -[ 20%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp +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; + | ^~~~~~~~ +[ 24%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp +[ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o cd 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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 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp +[ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 21%] 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++ -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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 -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/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp -[ 22%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp -[ 22%] 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 -[ 23%] 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/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 -[ 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-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 -[ 24%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp -[ 25%] 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/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp -[ 26%] 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 -[ 26%] 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 -[ 26%] 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 -[ 27%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -[ 28%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 -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 -[ 29%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ -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; | ^~~~~~~~ +[ 25%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +[ 26%] 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 +[ 27%] 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++ -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++ 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-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/Container/SequenceContainerIterator.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/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 +[ 29%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o +[ 29%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 +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 +[ 29%] 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 +[ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o +[ 30%] 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 +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 +[ 31%] 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 +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; | ^~~~~~~~ -[ 29%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +/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, @@ -645,85 +722,41 @@ /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/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; - | ^~~~~~~~ -[ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -/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; - | ^~~~~~~~ -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/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] - 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; - | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: -/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h: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; | ^~~~~~~~ +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; | ^~~~~~~~ -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; | ^~~~~~~~ +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; | ^~~~~~~~ -[ 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 -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; - | ^~~~~~~~ -[ 31%] 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 -[ 32%] 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 -[ 32%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 33%] 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/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: + 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; | ^~~~~~~~ @@ -736,12 +769,6 @@ /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-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 -[ 33%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 34%] 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 In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] @@ -757,8 +784,27 @@ /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-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++ -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 +[ 31%] 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 +[ 32%] 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 +[ 33%] 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 +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; + | ^~~~~~~~ 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=] @@ -776,28 +822,54 @@ /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; | ^~~~~~~~ -[ 35%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.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 +[ 34%] 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 +[ 34%] 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 +[ 35%] 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 +[ 35%] 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 +[ 36%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 +[ 37%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o +[ 37%] 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/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 +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 +[ 37%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +[ 38%] 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 +[ 39%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o +[ 39%] 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 +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 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; - | ^~~~~~~~ + 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: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; | ^~~~~~~~ -[ 36%] 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 -[ 36%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +/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; + | ^~~~~~~~ +[ 39%] 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++ -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 +[ 40%] 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 +[ 41%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o +[ 41%] 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 +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 +[ 42%] 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 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: @@ -816,28 +888,8 @@ | ^~~~~~~~ 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; - | ^~~~~~~~ -[ 37%] 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++ -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 -[ 37%] 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 -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: + 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; | ^~~~~~~~ @@ -850,58 +902,24 @@ /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-static.dir/Bpp/Seq/GeneticCode/GeneticCode.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 -[ 38%] 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 -[ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 40%] 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 -[ 40%] 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 -[ 40%] 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 -[ 41%] 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 -[ 42%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 -[ 42%] 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 +[ 43%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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; - | ^~~~~~~~ + 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; | ^~~~~~~~ -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; - | ^~~~~~~~ -[ 43%] 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 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: @@ -918,10 +936,6 @@ /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-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 -[ 44%] 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 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=] @@ -937,51 +951,56 @@ /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/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/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; - | ^~~~~~~~ + 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; | ^~~~~~~~ -[ 45%] 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/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; | ^~~~~~~~ +[ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +[ 44%] 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 +[ 45%] 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/Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 45%] 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 -[ 46%] 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 -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; + | ^~~~~~~~ +[ 45%] 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 +[ 45%] 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: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; | ^~~~~~~~ @@ -991,32 +1010,33 @@ /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; | ^~~~~~~~ -[ 46%] 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 +[ 46%] 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 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; - | ^~~~~~~~ +/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: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/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/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: +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ @@ -1026,12 +1046,26 @@ /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; | ^~~~~~~~ -[ 47%] 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 -[ 48%] 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 -[ 48%] 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 +[ 47%] 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++ -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/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; + | ^~~~~~~~ +[ 47%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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, @@ -1050,11 +1084,40 @@ /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; | ^~~~~~~~ -[ 48%] 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 -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=] +[ 47%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.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 +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))); + | ^ +[ 48%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +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, @@ -1062,52 +1125,68 @@ 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: + 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::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:71:27: + 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/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=] +/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))); | ^ -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 /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 /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; + | ^~~~~~~~ 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: + 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::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:70:27: + 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/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; +/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))); | ^ -[ 49%] 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 +[ 49%] 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/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=] @@ -1135,11 +1214,42 @@ /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))); | ^ -[ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o +[ 49%] 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 +[ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +[ 50%] 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 +[ 51%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +[ 51%] 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 +[ 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 +[ 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/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: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: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; | ^~~~~~~~ @@ -1154,15 +1264,12 @@ /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; | ^~~~~~~~ -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 -[ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -[ 51%] 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 -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 +[ 53%] 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 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: + 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; | ^~~~~~~~ @@ -1177,10 +1284,59 @@ /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; | ^~~~~~~~ -[ 51%] 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 -[ 52%] 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 +[ 54%] 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 +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp:40: +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] + 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; + | ^~~~~~~~ +/build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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-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 +[ 55%] 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 +[ 55%] 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/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))); + | ^ 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=] @@ -1208,10 +1364,46 @@ /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))); | ^ +[ 56%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +[ 56%] 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 +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))); + | ^ +[ 56%] 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 +[ 57%] 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 +[ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/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: + 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; | ^~~~~~~~ @@ -1226,33 +1418,16 @@ /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/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; - | ^~~~~~~~ -[ 52%] 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 -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: +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 +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; | ^~~~~~~~ @@ -1268,43 +1443,26 @@ 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: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; | ^~~~~~~~ -[ 53%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 53%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h: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; | ^~~~~~~~ -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 +[ 59%] 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 +[ 59%] 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: + 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; | ^~~~~~~~ @@ -1337,101 +1495,41 @@ /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-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 -[ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 55%] 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 -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; - | ^~~~~~~~ -[ 55%] 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 -[ 55%] 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++ -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 -[ 56%] 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 -[ 57%] 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 -[ 57%] 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 -[ 57%] 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/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; - | ^~~~~~~~ -[ 58%] 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 -[ 59%] 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 -[ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 60%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -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 /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/EchinodermMitochondrialGeneticCode.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::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:70:27: + 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))); | ^ -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 -/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; +/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/NexusIoSequence.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp:40: +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: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; | ^~~~~~~~ @@ -1441,19 +1539,23 @@ /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; | ^~~~~~~~ -[ 61%] 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 -[ 62%] 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/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: +[ 60%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o +[ 61%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o +[ 61%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o +[ 62%] 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/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 +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 +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 +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 +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; | ^~~~~~~~ @@ -1463,19 +1565,12 @@ /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; | ^~~~~~~~ -[ 62%] 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 -[ 62%] 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 -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: +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ -In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: +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; | ^~~~~~~~ @@ -1485,10 +1580,14 @@ /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; | ^~~~~~~~ +[ 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 +[ 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 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: + 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; | ^~~~~~~~ @@ -1503,145 +1602,6 @@ /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; | ^~~~~~~~ -[ 63%] 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++ -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 -[ 64%] 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 -[ 64%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 64%] 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 -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; - | ^~~~~~~~ -[ 64%] 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 -[ 65%] 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 -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))); - | ^ -[ 65%] 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/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))); - | ^ -[ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.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/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 -[ 68%] 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/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: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; - | ^~~~~~~~ -[ 68%] 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/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/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, @@ -1660,6 +1620,8 @@ /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; | ^~~~~~~~ +[ 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 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, @@ -1678,36 +1640,52 @@ /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; | ^~~~~~~~ -[ 69%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 69%] 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/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 -[ 69%] 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 -[ 70%] 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 -[ 71%] 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 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: + 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; | ^~~~~~~~ +[ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o +[ 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 +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 +[ 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 +In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ -[ 72%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.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 +/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; + | ^~~~~~~~ +[ 65%] 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++ -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 +[ 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 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, @@ -1726,46 +1704,66 @@ /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; | ^~~~~~~~ -[ 72%] 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 -/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, - | ^~~~~~ -[ 72%] 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 +[ 66%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o +cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 +[ 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 +[ 67%] 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 +[ 67%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o +[ 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++ -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 +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 +[ 69%] 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 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; | ^~~~~~~~ -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; | ^~~~~~~~ +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; + | ^~~~~~~~ +[ 69%] 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 +[ 70%] 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-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 +[ 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/GenBank.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp:40: + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ @@ -1780,32 +1778,53 @@ /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/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; | ^~~~~~~~ -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; | ^~~~~~~~ +[ 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/../Container/OrderedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, + from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h: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; + | ^~~~~~~~ +/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: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: +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; | ^~~~~~~~ @@ -1815,22 +1834,15 @@ /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/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 -[ 73%] 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 -[ 74%] 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 -[ 75%] 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 -[ 76%] 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/MaseTools.h:43, - from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: +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/MaseTools.h:44: +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; | ^~~~~~~~ @@ -1840,34 +1852,28 @@ /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; | ^~~~~~~~ -[ 76%] 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++ -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 -[ 76%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -[ 77%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 -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 -[ 78%] 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 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; | ^~~~~~~~ -[ 78%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 +/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; + | ^~~~~~~~ +[ 74%] 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 +[ 74%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.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/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 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, @@ -1886,29 +1892,12 @@ /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; | ^~~~~~~~ -[ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 -[ 79%] 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 -[ 80%] 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 -[ 80%] 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 -[ 80%] 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 -[ 81%] 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 -[ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -[ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -[ 83%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o -[ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.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 -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 -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 -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 -[ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o +[ 74%] 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 +[ 75%] 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 -[ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o +[ 76%] 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 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, @@ -1916,7 +1905,6 @@ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ -cd /build/reproducible-path/libbpp-seq-2.4.1/obj-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 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)' @@ -1928,28 +1916,76 @@ /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; | ^~~~~~~~ -[ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o +[ 76%] 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 +[ 77%] 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 -[ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o +[ 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 -[ 86%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o +[ 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 -[ 86%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o +[ 79%] 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 +[ 80%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.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/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 +[ 80%] 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/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 +[ 80%] 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 -[ 87%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o +[ 81%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o +[ 82%] Building CXX object src/CMakeFiles/bpp-seq-static.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/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 -[ 87%] 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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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 +[ 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 -[ 88%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o +[ 83%] 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 -[ 89%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -[ 89%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o +[ 83%] 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 +/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, + | ^~~~~~ +[ 84%] 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 +[ 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 -[ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o +[ 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-shared.dir/Bpp/Seq/SymbolListTools.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 -[ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o +[ 87%] 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 +[ 88%] 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-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++ -I/build/reproducible-path/libbpp-seq-2.4.1/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-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 +[ 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 /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)); @@ -1964,12 +2000,12 @@ /usr/include/c++/15/bits/stl_algo.h:772:5: note: declared here 772 | remove(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~ -[ 91%] Linking CXX static library libbpp-seq.a +[ 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" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/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 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"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 @@ -1977,11 +2013,11 @@ 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[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_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' +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=" +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 -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' @@ -1996,43 +2032,39 @@ 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[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' -make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/build -make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.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 -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.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 -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_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' +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 -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-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[3]: Entering 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[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' -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' -[ 93%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -[ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -[ 95%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o -[ 96%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.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_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_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 -[ 96%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.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_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 +[ 93%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o +[ 93%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.cpp.o +[ 94%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.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_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 -[ 97%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.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_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_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 -[ 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_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 +[ 97%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o +[ 97%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o +[ 97%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o +[ 98%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.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_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 -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' -[ 98%] Built target bpp-seq-static +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_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_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 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, @@ -2053,18 +2085,18 @@ 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: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; | ^~~~~~~~ +/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/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, @@ -2083,49 +2115,53 @@ /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; | ^~~~~~~~ -[ 99%] Linking CXX executable test_walker -[ 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 -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_containers +[ 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 -/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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_walker.dir/link.d CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 -[ 99%] Linking CXX executable test_alphabets +[ 98%] 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 +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' -/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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_sequences.dir/link.d CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 +[ 99%] Linking CXX executable test_alphabets +[ 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 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 -make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_containers.dir/link.d CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_sequences.dir/link.d CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [ 99%] Built target test_sequences -[ 99%] Built target test_walker [ 99%] Built target test_containers -/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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alphabets.dir/link.d CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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%] Built target bpp-seq-static [ 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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 +[ 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 +/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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_walker.dir/link.d CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 +/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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alphabets.dir/link.d CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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 [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 -[100%] 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 -/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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alignment_scores.dir/link.d CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -o test_alignment_scores -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 +[100%] Built target test_alphabets +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' -[100%] Built target test_alignment_scores +[100%] Built target test_bowker /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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_io.dir/link.d CMakeFiles/test_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' [100%] Built target test_io +/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 -rdynamic -Wl,--dependency-file=CMakeFiles/test_alignment_scores.dir/link.d CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -o test_alignment_scores -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-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' +[100%] Built target test_alignment_scores 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 + cd obj-x86_64-linux-gnu && make -j42 test ARGS\+=--verbose ARGS\+=-j42 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 +/usr/bin/ctest --force-new-ctest-process --verbose -j42 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 @@ -2321,18 +2357,18 @@ 5: 100 1209 5: 100 1209 6/7 Test #5: test_io .......................... Passed 0.03 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%0.0068 0.0448 0.096 0.504 -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%0.0102 0.0504 0.1044 0.5098 -7/7 Test #3: test_bowker ...................... Passed 15.18 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%0.01 0.049 0.0956 0.5016 +3: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0096 0.0486 0.0986 0.5116 +7/7 Test #3: test_bowker ...................... Passed 15.16 sec 100% tests passed, 0 tests failed out of 7 -Total Test time (real) = 15.19 sec +Total Test time (real) = 15.16 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" + cd obj-x86_64-linux-gnu && make -j42 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 @@ -2350,139 +2386,139 @@ -- 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/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/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/GranthamAAVolumeIndex.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/AAChouFasmanTurnIndex.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/MiyataAAChemicalDistance.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/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/AAIndex1Entry.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEA1030Index.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAMassIndex.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex1.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/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/AlphabetIndex2.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/SimpleScore.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/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/DefaultNucleotideScore.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/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/AlphabetIndex/BLOSUM50.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/AAIndex2Entry.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/Container +-- 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/SequenceContainerExceptions.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/VectorSiteContainer.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/OrderedSequenceContainer.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerTools.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerIterator.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainer.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/VectorSequenceContainer.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/SequenceContainer.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/AbstractSequenceContainer.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/Transliterator.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/AlphabetState.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/DNA.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LexicalAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetNumericState.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/AlphabetExceptions.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/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/NucleicAlphabetState.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/CodonAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LetterAlphabet.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/ProteicAlphabetState.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/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/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/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/NucleicAcidsReplication.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/DNAToRNA.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/GeneticCode +-- 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/VertebrateMitochondrialGeneticCode.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/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/MoldMitochondrialGeneticCode.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/SequenceWithQualityTools.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/SequenceExceptions.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/SequenceWalker.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/CodonSiteTools.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/SiteExceptions.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/SymbolList.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/SequenceTools.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/Fasta.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Dcse.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/PhredPhd.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/OSequenceStream.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/MaseTools.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/NexusIoSequence.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/Stockholm.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/BppOSequenceStreamReaderFormat.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/BppOAlignmentReaderFormat.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/AbstractIAlignment.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/BppOSequenceWriterFormat.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/SequenceFileIndex.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/StreamSequenceIterator.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/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/BppOAlignmentWriterFormat.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/BppOAlphabetIndex2Format.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex1Format.h +-- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractISequence.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/Phylip.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/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' @@ -2540,12 +2576,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/550582/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/550582/tmp/hooks/B01_cleanup finished 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/510047 and its subdirectories -I: Current time: Mon Sep 15 21:36:17 -12 2025 -I: pbuilder-time-stamp: 1758015377 +I: removing directory /srv/workspace/pbuilder/550582 and its subdirectories +I: Current time: Tue Oct 20 06:00:36 +14 2026 +I: pbuilder-time-stamp: 1792425636 Compressing the 2nd log... /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/libbpp-seq_2.4.1-13.diff: 95.3% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/logdiffs/unstable/amd64/libbpp-seq_2.4.1-13.diff.gz b2/build.log: 94.0% -- replaced with stdout Compressing the 1st log... b1/build.log: 93.9% -- replaced with stdout Tue Sep 16 09:37:38 UTC 2025 I: diffoscope 306 will be used to compare the two builds: ++ date -u +%s + DIFFOSCOPE_STAMP=/var/log/reproducible-builds/diffoscope_stamp_libbpp-seq_unstable_amd64_1758015458 + touch /var/log/reproducible-builds/diffoscope_stamp_libbpp-seq_unstable_amd64_1758015458 + RESULT=0 + systemd-run '--description=diffoscope on libbpp-seq/2.4.1-13 in unstable/amd64' --slice=rb-build-diffoscope.slice -u rb-diffoscope-amd64_11-67713 '--property=SuccessExitStatus=1 124' --user --send-sighup --pipe --wait -E TMPDIR timeout 155m nice schroot --directory /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn --run-session -c jenkins-reproducible-unstable-diffoscope-a3e700b6-11f4-4212-860a-ac9ba27b31f8 -- sh -c 'export TMPDIR=/srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/dbd-tmp-slG8ozG ; timeout 150m diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/libbpp-seq_2.4.1-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/libbpp-seq_2.4.1-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/libbpp-seq_2.4.1-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b1/libbpp-seq_2.4.1-13_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b2/libbpp-seq_2.4.1-13_amd64.changes' + false + set +x Running as unit: rb-diffoscope-amd64_11-67713.service; invocation ID: 182b11b3076e4ba3b50da6d449fc656f # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/libbpp-seq_2.4.1-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/libbpp-seq_2.4.1-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/libbpp-seq_2.4.1-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b1/libbpp-seq_2.4.1-13_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.Ao7rVHRn/b2/libbpp-seq_2.4.1-13_amd64.changes ## command (total time: 0.053s) 0.053s 1 call cmp (internal) ## has_same_content_as (total time: 0.053s) 0.053s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.055s) 0.055s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 299ms CPU time consumed: 200ms Memory peak: 18.9M (swap: 0B) _ _ _ _ | (_) |__ | |__ _ __ _ __ ___ ___ __ _ | | | '_ \| '_ \| '_ \| '_ \ _____/ __|/ _ \/ _` | | | | |_) | |_) | |_) | |_) |_____\__ \ __/ (_| | |_|_|_.__/|_.__/| .__/| .__/ |___/\___|\__, | |_| |_| |_| Tue Sep 16 09:41:47 UTC 2025 I: diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Sep 16 09:41:47 UTC 2025 I: libbpp-seq from unstable built successfully and reproducibly on amd64. INSERT 0 1 INSERT 0 1 DELETE 1 [2025-09-16 09:41:48] INFO: Starting at 2025-09-16 09:41:48.527089 [2025-09-16 09:41:48] INFO: Generating the pages of 1 package(s) [2025-09-16 09:41:49] CRITICAL: https://tests.reproducible-builds.org/debian/unstable/amd64/libbpp-seq didn't produce a buildlog, even though it has been built. [2025-09-16 09:41:49] INFO: Finished at 2025-09-16 09:41:49.103156, took: 0:00:00.576074 Tue Sep 16 09:41:49 UTC 2025 - successfully updated the database and updated https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/libbpp-seq.html Tue Sep 16 09:41:49 UTC 2025 I: Removing signed libbpp-seq_2.4.1-13_amd64.buildinfo.asc files: removed './b1/libbpp-seq_2.4.1-13_amd64.buildinfo.asc' removed './b2/libbpp-seq_2.4.1-13_amd64.buildinfo.asc' 1758015709 amd64 unstable libbpp-seq Starting cleanup. /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/libbpp-seq_2.4.1-13.rbuild.log: 93.2% -- replaced with /var/lib/jenkins/userContent/reproducible/debian/rbuild/unstable/amd64/libbpp-seq_2.4.1-13.rbuild.log.gz [2025-09-16 09:41:50] INFO: Starting at 2025-09-16 09:41:50.130626 [2025-09-16 09:41:50] INFO: Generating the pages of 1 package(s) [2025-09-16 09:41:50] INFO: Finished at 2025-09-16 09:41:50.527772, took: 0:00:00.397153 All cleanup done. Tue Sep 16 09:41:50 UTC 2025 - total duration: 0h 7m 15s. Tue Sep 16 09:41:50 UTC 2025 - reproducible_build.sh stopped running as /tmp/jenkins-script-7L1hdYDI, removing. Finished with result: success Main processes terminated with: code=exited, status=0/SUCCESS Service runtime: 7min 18.368s CPU time consumed: 4.707s Memory peak: 63.4M (swap: 0B)