sbuild (Debian sbuild) 0.81.2+deb11u1 (31 August 2022) on debian-ci-siliconvalley +==============================================================================+ | fastml 3.11-3 (arm64) Mon, 19 Dec 2022 01:50:32 +0000 | +==============================================================================+ Package: fastml Version: 3.11-3 Source Version: 3.11-3 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-8129ee96-4255-411b-8a83-9abc34a4df74' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-RZTu8Z/resolver-vttBbW' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://localhost:3142/debian sid InRelease Get:2 http://localhost:3142/debian sid/main arm64 Packages [9246 kB] Fetched 9246 kB in 1s (8750 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'fastml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fastml.git Please use: git clone https://salsa.debian.org/med-team/fastml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 861 kB of source archives. Get:1 http://localhost:3142/debian sid/main fastml 3.11-3 (dsc) [1897 B] Get:2 http://localhost:3142/debian sid/main fastml 3.11-3 (tar) [849 kB] Get:3 http://localhost:3142/debian sid/main fastml 3.11-3 (diff) [9984 B] Fetched 861 kB in 0s (0 B/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/fastml-RZTu8Z/fastml-3.11' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-RZTu8Z' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [403 B] Get:5 copy:/<>/apt_archive ./ Packages [490 B] Fetched 1850 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-12-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-base:arm64 gcc-12-aarch64-linux-gnu gcc-12-aarch64-linux-gnu-base gcc-12-base:arm64 gcc-12-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:arm64 libgcc-12-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libicu72 libio-string-perl libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libnsl-dev:arm64 libnsl2:arm64 libpipeline1 libssl3:arm64 libstdc++-11-dev:arm64 libstdc++-12-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-12-locales cpp-12-doc cpp-doc dh-make binutils-multiarch gcc-12-doc manpages-dev flex bison gdb-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 krb5-doc:arm64 krb5-user:arm64 libstdc++-11-doc:arm64 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:arm64 libarchive-cpio-perl krb5-locales:arm64 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-12-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-11-base:arm64 gcc-12-aarch64-linux-gnu gcc-12-aarch64-linux-gnu-base gcc-12-base:arm64 gcc-12-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:arm64 libgcc-12-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhwasan0:arm64 libhwasan0-arm64-cross libicu72 libio-string-perl libitm1:arm64 libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64 libkrb5support0:arm64 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross libmagic-mgc libmagic1 libnsl-dev:arm64 libnsl2:arm64 libpipeline1 libssl3:arm64 libstdc++-11-dev:arm64 libstdc++-12-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libsub-override-perl libtirpc-dev:arm64 libtirpc3:arm64 libtool libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:arm64 sensible-utils ucf 0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded. Need to get 94.2 MB of archives. After this operation, 394 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get:3 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17 [21.5 kB] Get:4 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.41-4 [295 kB] Get:5 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.41-4 [129 kB] Get:6 http://localhost:3142/debian sid/main amd64 file amd64 1:5.41-4 [67.0 kB] Get:7 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-10 [160 kB] Get:8 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:9 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-9 [916 kB] Get:10 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38.1-4 [86.2 kB] Get:11 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:12 http://localhost:3142/debian sid/main amd64 man-db amd64 2.11.1-1 [1384 kB] Get:13 http://localhost:3142/debian sid/main amd64 ucf all 3.0043 [74.0 kB] Get:14 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-1 [291 kB] Get:15 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-2 [343 kB] Get:16 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:17 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:18 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-10 [495 kB] Get:19 http://localhost:3142/debian sid/main amd64 binutils-aarch64-linux-gnu amd64 2.39.50.20221208-5 [3389 kB] Get:20 http://localhost:3142/debian sid/main amd64 gcc-12-aarch64-linux-gnu-base amd64 12.2.0-9cross2 [37.3 kB] Get:21 http://localhost:3142/debian sid/main amd64 cpp-12-aarch64-linux-gnu amd64 12.2.0-9cross2 [9151 kB] Get:22 http://localhost:3142/debian sid/main amd64 cpp-aarch64-linux-gnu amd64 4:12.2.0-1 [17.1 kB] Get:23 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:24 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base all 12.2.0-9cross2 [32.8 kB] Get:25 http://localhost:3142/debian sid/main amd64 libc6-arm64-cross all 2.36-3cross1 [1002 kB] Get:26 http://localhost:3142/debian sid/main amd64 libgcc-s1-arm64-cross all 12.2.0-9cross2 [34.8 kB] Get:27 http://localhost:3142/debian sid/main amd64 libgomp1-arm64-cross all 12.2.0-9cross2 [102 kB] Get:28 http://localhost:3142/debian sid/main amd64 libitm1-arm64-cross all 12.2.0-9cross2 [23.4 kB] Get:29 http://localhost:3142/debian sid/main amd64 libatomic1-arm64-cross all 12.2.0-9cross2 [9272 B] Get:30 http://localhost:3142/debian sid/main amd64 libasan8-arm64-cross all 12.2.0-9cross2 [2097 kB] Get:31 http://localhost:3142/debian sid/main amd64 liblsan0-arm64-cross all 12.2.0-9cross2 [925 kB] Get:32 http://localhost:3142/debian sid/main amd64 libtsan2-arm64-cross all 12.2.0-9cross2 [2180 kB] Get:33 http://localhost:3142/debian sid/main amd64 libstdc++6-arm64-cross all 12.2.0-9cross2 [513 kB] Get:34 http://localhost:3142/debian sid/main amd64 libubsan1-arm64-cross all 12.2.0-9cross2 [862 kB] Get:35 http://localhost:3142/debian sid/main amd64 libhwasan0-arm64-cross all 12.2.0-9cross2 [997 kB] Get:36 http://localhost:3142/debian sid/main amd64 libgcc-12-dev-arm64-cross all 12.2.0-9cross2 [959 kB] Get:37 http://localhost:3142/debian sid/main amd64 gcc-12-aarch64-linux-gnu amd64 12.2.0-9cross2 [18.0 MB] Get:38 http://localhost:3142/debian sid/main amd64 gcc-aarch64-linux-gnu amd64 4:12.2.0-1 [1452 B] Get:39 http://localhost:3142/debian sid/main amd64 linux-libc-dev-arm64-cross all 6.0.6-2cross1 [1778 kB] Get:40 http://localhost:3142/debian sid/main amd64 libc6-dev-arm64-cross all 2.36-3cross1 [1422 kB] Get:41 http://localhost:3142/debian sid/main amd64 libstdc++-12-dev-arm64-cross all 12.2.0-9cross2 [1975 kB] Get:42 http://localhost:3142/debian sid/main amd64 g++-12-aarch64-linux-gnu amd64 12.2.0-9cross2 [10.1 MB] Get:43 http://localhost:3142/debian sid/main amd64 g++-aarch64-linux-gnu amd64 4:12.2.0-1 [1176 B] Get:44 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:45 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-3.1 [11.8 kB] Get:46 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:47 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b2 [687 kB] Get:48 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:49 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:50 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:51 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:52 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:53 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:54 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:55 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:56 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:57 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:58 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:59 http://localhost:3142/debian sid/main amd64 crossbuild-essential-arm64 all 12.9 [6708 B] Get:60 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.3 [81.1 kB] Get:61 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-5 [517 kB] Get:62 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:63 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:64 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get:65 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.0-2 [19.4 kB] Get:66 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.0-2 [8556 B] Get:67 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.188-1 [172 kB] Get:68 http://localhost:3142/debian sid/main amd64 dwz amd64 0.14+20220924-2 [109 kB] Get:69 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-10 [1300 kB] Get:70 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:71 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:72 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.3 [942 kB] Get:73 http://localhost:3142/debian sid/main arm64 gcc-11-base arm64 11.3.0-8 [209 kB] Get:74 http://localhost:3142/debian sid/main arm64 gcc-12-base arm64 12.2.0-10 [37.2 kB] Get:75 http://localhost:3142/debian sid/main arm64 libgcc-s1 arm64 12.2.0-10 [34.8 kB] Get:76 http://localhost:3142/debian sid/main arm64 libc6 arm64 2.36-6 [2313 kB] Get:77 http://localhost:3142/debian sid/main arm64 libasan6 arm64 11.3.0-8 [1952 kB] Get:78 http://localhost:3142/debian sid/main arm64 libatomic1 arm64 12.2.0-10 [9536 B] Get:79 http://localhost:3142/debian sid/main arm64 linux-libc-dev arm64 6.0.12-1 [1672 kB] Get:80 http://localhost:3142/debian sid/main arm64 libcrypt1 arm64 1:4.4.33-1 [90.0 kB] Get:81 http://localhost:3142/debian sid/main arm64 libcrypt-dev arm64 1:4.4.33-1 [121 kB] Get:82 http://localhost:3142/debian sid/main arm64 libcom-err2 arm64 1.46.6~rc1-1+b1 [14.7 kB] Get:83 http://localhost:3142/debian sid/main arm64 libkrb5support0 arm64 1.20.1-1 [31.5 kB] Get:84 http://localhost:3142/debian sid/main arm64 libk5crypto3 arm64 1.20.1-1 [78.9 kB] Get:85 http://localhost:3142/debian sid/main arm64 libkeyutils1 arm64 1.6.3-1 [15.7 kB] Get:86 http://localhost:3142/debian sid/main arm64 libssl3 arm64 3.0.7-1 [1795 kB] Get:87 http://localhost:3142/debian sid/main arm64 libkrb5-3 arm64 1.20.1-1 [313 kB] Get:88 http://localhost:3142/debian sid/main arm64 libgssapi-krb5-2 arm64 1.20.1-1 [123 kB] Get:89 http://localhost:3142/debian sid/main arm64 libtirpc3 arm64 1.3.3+ds-1 [80.9 kB] Get:90 http://localhost:3142/debian sid/main arm64 libnsl2 arm64 1.3.0-2 [36.9 kB] Get:91 http://localhost:3142/debian sid/main arm64 libtirpc-dev arm64 1.3.3+ds-1 [194 kB] Get:92 http://localhost:3142/debian sid/main arm64 libnsl-dev arm64 1.3.0-2 [66.1 kB] Get:93 http://localhost:3142/debian sid/main arm64 libc6-dev arm64 2.36-6 [1426 kB] Get:94 http://localhost:3142/debian sid/main arm64 libgomp1 arm64 12.2.0-10 [104 kB] Get:95 http://localhost:3142/debian sid/main arm64 libitm1 arm64 12.2.0-10 [23.9 kB] Get:96 http://localhost:3142/debian sid/main arm64 liblsan0 arm64 12.2.0-10 [926 kB] Get:97 http://localhost:3142/debian sid/main arm64 libtsan0 arm64 11.3.0-8 [1958 kB] Get:98 http://localhost:3142/debian sid/main arm64 libstdc++6 arm64 12.2.0-10 [557 kB] Get:99 http://localhost:3142/debian sid/main arm64 libubsan1 arm64 12.2.0-10 [862 kB] Get:100 http://localhost:3142/debian sid/main arm64 libhwasan0 arm64 12.2.0-10 [999 kB] Get:101 http://localhost:3142/debian sid/main arm64 libgcc-11-dev arm64 11.3.0-8 [933 kB] Get:102 http://localhost:3142/debian sid/main arm64 libstdc++-11-dev arm64 11.3.0-8 [1927 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 94.2 MB in 1s (181 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 15723 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.17_all.deb ... Unpacking sensible-utils (0.0.17) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.41-4_amd64.deb ... Unpacking libmagic-mgc (1:5.41-4) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.41-4_amd64.deb ... Unpacking libmagic1:amd64 (1:5.41-4) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.41-4_amd64.deb ... Unpacking file (1:5.41-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-10_amd64.deb ... Unpacking gettext-base (0.21-10) ... 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Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-3.1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up libc6-arm64-cross (2.36-3cross1) ... Setting up autopoint (0.21-10) ... Setting up libitm1-arm64-cross (12.2.0-9cross2) ... Setting up autoconf (2.71-2) ... Setting up linux-libc-dev-arm64-cross (6.0.6-2cross1) ... Setting up sensible-utils (0.0.17) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libelf1:amd64 (0.188-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b2) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up libgcc-s1-arm64-cross (12.2.0-9cross2) ... Setting up libatomic1-arm64-cross (12.2.0-9cross2) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.0-2) ... Setting up liblsan0-arm64-cross (12.2.0-9cross2) ... Setting up libgomp1-arm64-cross (12.2.0-9cross2) ... Setting up gettext (0.21-10) ... Setting up cpp-12-aarch64-linux-gnu (12.2.0-9cross2) ... Setting up libtool (2.4.7-5) ... Setting up libhwasan0-arm64-cross (12.2.0-9cross2) ... Setting up libc6-dev-arm64-cross (2.36-3cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libstdc++6-arm64-cross (12.2.0-9cross2) ... Setting up dh-autoreconf (20) ... Setting up cpp-aarch64-linux-gnu (4:12.2.0-1) ... Setting up ucf (3.0043) ... Setting up dh-strip-nondeterminism (1.13.0-2) ... Setting up dwz (0.14+20220924-2) ... Setting up groff-base (1.22.4-9) ... Setting up libasan8-arm64-cross (12.2.0-9cross2) ... Setting up libtsan2-arm64-cross (12.2.0-9cross2) ... Setting up libubsan1-arm64-cross (12.2.0-9cross2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.11.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-12-dev-arm64-cross (12.2.0-9cross2) ... Setting up gcc-12-aarch64-linux-gnu (12.2.0-9cross2) ... Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-aarch64-linux-gnu (4:12.2.0-1) ... Setting up debhelper (13.11.3) ... Setting up libstdc++-12-dev-arm64-cross (12.2.0-9cross2) ... Setting up libxml-simple-perl (2.25-2) ... Setting up g++-12-aarch64-linux-gnu (12.2.0-9cross2) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-aarch64-linux-gnu (4:12.2.0-1) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-arm64 (12.9) ... Setting up libgcc-s1:arm64 (12.2.0-10) ... Setting up libc6:arm64 (2.36-6) ... Setting up libhwasan0:arm64 (12.2.0-10) ... Setting up libstdc++6:arm64 (12.2.0-10) ... Setting up liblsan0:arm64 (12.2.0-10) ... Setting up libitm1:arm64 (12.2.0-10) ... Setting up libtsan0:arm64 (11.3.0-8) ... Setting up libkeyutils1:arm64 (1.6.3-1) ... Setting up libssl3:arm64 (3.0.7-1) ... Setting up libcrypt1:arm64 (1:4.4.33-1) ... Setting up libcom-err2:arm64 (1.46.6~rc1-1+b1) ... Setting up libgomp1:arm64 (12.2.0-10) ... Setting up libasan6:arm64 (11.3.0-8) ... Setting up libkrb5support0:arm64 (1.20.1-1) ... Setting up libatomic1:arm64 (12.2.0-10) ... Setting up libk5crypto3:arm64 (1.20.1-1) ... Setting up libubsan1:arm64 (12.2.0-10) ... Setting up libgcc-11-dev:arm64 (11.3.0-8) ... Setting up libcrypt-dev:arm64 (1:4.4.33-1) ... Setting up libkrb5-3:arm64 (1.20.1-1) ... Setting up libgssapi-krb5-2:arm64 (1.20.1-1) ... Setting up libtirpc3:arm64 (1.3.3+ds-1) ... Setting up libtirpc-dev:arm64 (1.3.3+ds-1) ... Setting up libnsl2:arm64 (1.3.0-2) ... Setting up libnsl-dev:arm64 (1.3.0-2) ... Setting up libc6-dev:arm64 (2.36-6) ... Setting up libstdc++-11-dev:arm64 (11.3.0-8) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.36-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) amd64 (x86_64) Toolchain package versions: binutils_2.39.50.20221208-5 dpkg-dev_1.21.12 g++-11_11.3.0-8 g++-12_12.2.0-10 gcc-11_11.3.0-8 gcc-12_12.2.0-10 libc6-dev_2.36-6 libstdc++-11-dev_11.3.0-8 libstdc++-12-dev_12.2.0-10 libstdc++-12-dev-arm64-cross_12.2.0-9cross2 libstdc++6_12.2.0-10 libstdc++6-arm64-cross_12.2.0-9cross2 linux-libc-dev_6.0.12-1 Package versions: adduser_3.129 apt_2.5.4 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-10 autotools-dev_20220109.1 base-files_12.3 base-passwd_3.6.1 bash_5.2-2+b1 binutils_2.39.50.20221208-5 binutils-aarch64-linux-gnu_2.39.50.20221208-5 binutils-common_2.39.50.20221208-5 binutils-x86-64-linux-gnu_2.39.50.20221208-5 bsdextrautils_2.38.1-4 bsdutils_1:2.38.1-4 build-essential_12.9 bzip2_1.0.8-5+b1 coreutils_9.1-1 cpp_4:12.2.0-1 cpp-11_11.3.0-8 cpp-12_12.2.0-10 cpp-12-aarch64-linux-gnu_12.2.0-9cross2 cpp-aarch64-linux-gnu_4:12.2.0-1 cross-config_2.6.20 crossbuild-essential-arm64_12.9 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.80 debhelper_13.11.3 debian-archive-keyring_2021.1.1 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-2 diffutils_1:3.8-2 dpkg_1.21.12 dpkg-cross_2.6.20 dpkg-dev_1.21.12 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1+b1 fakeroot_1.30.1-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1 g++-11_11.3.0-8 g++-12_12.2.0-10 g++-12-aarch64-linux-gnu_12.2.0-9cross2 g++-aarch64-linux-gnu_4:12.2.0-1 gcc_4:12.2.0-1 gcc-11_11.3.0-8 gcc-11-base_11.3.0-8 gcc-12_12.2.0-10 gcc-12-aarch64-linux-gnu_12.2.0-9cross2 gcc-12-aarch64-linux-gnu-base_12.2.0-9cross2 gcc-12-base_12.2.0-10 gcc-12-cross-base_12.2.0-9cross2 gcc-9-base_9.5.0-2+b2 gcc-aarch64-linux-gnu_4:12.2.0-1 gettext_0.21-10 gettext-base_0.21-10 gpgv_2.2.40-1 grep_3.8-3 groff-base_1.22.4-9 gzip_1.12-1 hostname_3.23 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-2 libapt-pkg6.0_2.5.4 libarchive-zip-perl_1.68-1 libasan6_11.3.0-8 libasan8_12.2.0-10 libasan8-arm64-cross_12.2.0-9cross2 libatomic1_12.2.0-10 libatomic1-arm64-cross_12.2.0-9cross2 libattr1_1:2.5.1-3 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1+b2 libbinutils_2.39.50.20221208-5 libblkid1_2.38.1-4 libbz2-1.0_1.0.8-5+b1 libc-bin_2.36-6 libc-dev-bin_2.36-6 libc6_2.36-6 libc6-arm64-cross_2.36-3cross1 libc6-dev_2.36-6 libc6-dev-arm64-cross_2.36-3cross1 libcap-ng0_0.8.3-1+b2 libcap2_1:2.66-2 libcc1-0_12.2.0-10 libcom-err2_1.46.6~rc1-1+b1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.33-1 libcrypt1_1:4.4.33-1 libctf-nobfd0_2.39.50.20221208-5 libctf0_2.39.50.20221208-5 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.265 libdebhelper-perl_13.11.3 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.21.12 libelf1_0.188-1 libext2fs2_1.46.6~rc1-1+b1 libfakeroot_1.30.1-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.0-2 libfile-which-perl_1.27-2 libgcc-11-dev_11.3.0-8 libgcc-12-dev_12.2.0-10 libgcc-12-dev-arm64-cross_12.2.0-9cross2 libgcc-s1_12.2.0-10 libgcc-s1-arm64-cross_12.2.0-9cross2 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-4 libgomp1_12.2.0-10 libgomp1-arm64-cross_12.2.0-9cross2 libgpg-error0_1.46-1 libgprofng0_2.39.50.20221208-5 libgssapi-krb5-2_1.20.1-1 libhogweed6_3.8.1-2 libhwasan0_12.2.0-10 libhwasan0-arm64-cross_12.2.0-9cross2 libicu72_72.1-3 libidn2-0_2.3.3-1+b1 libio-string-perl_1.08-3.1 libisl23_0.25-1 libitm1_12.2.0-10 libitm1-arm64-cross_12.2.0-9cross2 libjansson4_2.14-2 libk5crypto3_1.20.1-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20.1-1 libkrb5support0_1.20.1-1 liblocale-gettext-perl_1.07-5 liblsan0_12.2.0-10 liblsan0-arm64-cross_12.2.0-9cross2 liblz4-1_1.9.4-1 liblzma5_5.4.0-0.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmd0_1.0.4-2 libmount1_2.38.1-4 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libnettle8_3.8.1-2 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.24.1-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpcre2-8-0_10.40-3 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libperl5.36_5.36.0-6 libpipeline1_1.5.7-1 libquadmath0_12.2.0-10 libseccomp2_2.5.4-1+b2 libselinux1_3.4-1+b3 libsemanage-common_3.4-1 libsemanage2_3.4-1+b3 libsepol2_3.4-2 libsmartcols1_2.38.1-4 libss2_1.46.6~rc1-1+b1 libssl3_3.0.7-1 libstdc++-11-dev_11.3.0-8 libstdc++-12-dev_12.2.0-10 libstdc++-12-dev-arm64-cross_12.2.0-9cross2 libstdc++6_12.2.0-10 libstdc++6-arm64-cross_12.2.0-9cross2 libsub-override-perl_0.09-4 libsystemd0_252.3-2 libtasn1-6_4.19.0-2 libtext-glob-perl_0.11-3 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan0_11.3.0-8 libtsan2_12.2.0-10 libtsan2-arm64-cross_12.2.0-9cross2 libubsan1_12.2.0-10 libubsan1-arm64-cross_12.2.0-9cross2 libuchardet0_0.0.7-1 libudev1_252.3-2 libunistring2_1.0-2 libuuid1_2.38.1-4 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.1+b2 libxxhash0_0.8.1-1 libyaml-perl_1.30-2 libzstd1_1.5.2+dfsg-1 linux-libc-dev_6.0.12-1 linux-libc-dev-arm64-cross_6.0.6-2cross1 login_1:4.13+dfsg1-1 logsave_1.46.6~rc1-1+b1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.1-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-4 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 passwd_1:4.13+dfsg1-1 patch_2.7.6-7 perl_5.36.0-6 perl-base_5.36.0-6 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-6 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.05-7 tar_1.34+dfsg-1.1 tzdata_2022f-1 ucf_3.0043 usrmerge_35 util-linux_2.38.1-4 util-linux-extra_2.38.1-4 xz-utils_5.4.0-0.1 zlib1g_1:1.2.13.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: fastml Binary: fastml Architecture: any Version: 3.11-3 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fastml.tau.ac.il/ Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/fastml Vcs-Git: https://salsa.debian.org/med-team/fastml.git Build-Depends: debhelper-compat (= 13) Package-List: fastml deb science optional arch=any Checksums-Sha1: 2bc5d72d636c37c0890c36b7e426d24131bfac8d 849058 fastml_3.11.orig.tar.gz 048ab93c1c1d67bea8c949b2026e9a25dc117a1c 9984 fastml_3.11-3.debian.tar.xz Checksums-Sha256: 2d1ec87116eae1163177631ad39083db01cdd78ffb8d119bebbdbb6a43e99451 849058 fastml_3.11.orig.tar.gz f9a00304da244a0bc0561a3723a633bc9690766687c46c11ea8af18aa5223617 9984 fastml_3.11-3.debian.tar.xz Files: 4443e346151ff347816dcba7e700212d 849058 fastml_3.11.orig.tar.gz ba33f9cb4200207ddb91e8e805b80ae8 9984 fastml_3.11-3.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl/bbYMRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtF3/Q//bwZ0+AM/yZTvJmHajmsFhoN8mmoSXk4W W3tiORMO/GrGqrQqfhzqMeLUKg3hVEKp2K5KOc1p86bnrVfhcG+KHJDo6c9jCG50 /e0gb3MYP4yQjaol0WQAZGZRASG+eAwqKe0iN0KsuB0wjbzyf4EMDiXq8PKA4VjD I3Oi9Ed9oa7+KuaxkijbCrbrzWdvQJm1/QcULIQf8TNRLvsZT8q2UJa3wAy50KL9 j5FZgqja+2M9bQP5k3ZYXwR4kgLAU7hSTRhCvPHardAPtM7UZkgf2r8T/YEuATfu 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fastml_3.11-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying gcc_5.patch dpkg-source: info: applying fix_makefile4test.patch dpkg-source: info: applying fix_intall_target.patch dpkg-source: info: applying spelling.patch dpkg-source: info: applying change_to_tests_dir_only_if_existing.patch dpkg-source: info: applying skip_failing_tests.patch dpkg-source: info: applying remove-template-depth.patch dpkg-source: info: applying cross.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.arm64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-8129ee96-4255-411b-8a83-9abc34a4df74 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarm64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-3 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j1 clean make[2]: Entering directory '/<>' cd libs;make clean make[3]: Entering directory '/<>/libs' cd phylogeny && make clean make[4]: Entering directory '/<>/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Leaving directory '/<>/libs/phylogeny' make[3]: Leaving directory '/<>/libs' cd programs;make clean make[3]: Entering directory '/<>/programs' cd fastml && make clean make[4]: Entering directory '/<>/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Leaving directory '/<>/programs/fastml' cd gainLoss && make clean make[4]: Entering directory '/<>/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make clean make[4]: Entering directory '/<>/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/<>/programs/indelCoder' make[3]: Leaving directory '/<>/programs' make[2]: Leaving directory '/<>' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc make[1]: Entering directory '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/libs/phylogeny' making depend aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp bestAlpha.cpp: In constructor ‘bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)’: bestAlpha.cpp:371:17: warning: variable ‘oldA’ set but not used [-Wunused-but-set-variable] 371 | MDOUBLE oldA=0; | ^~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp bestAlphaManyTrees.cpp: In function ‘void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector&, std::vector&, const std::vector*>*, std::vector&, double&, int, double)’: bestAlphaManyTrees.cpp:184:17: warning: variable ‘ax’ set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ bestAlphaManyTrees.cpp:184:20: warning: variable ‘bx’ set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ bestAlphaManyTrees.cpp:184:23: warning: variable ‘cx’ set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h: In constructor ‘computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::string&, VVVdouble&, int, double, bool)’: computeSubstitutionCounts.h:57:19: warning: ‘computeSubstitutionCounts::_LpostPerSpPerCat’ will be initialized after [-Wreorder] 57 | VVVdouble _LpostPerSpPerCat; // _LpostPerSpPerCat[sp][rateCat][pos] | ^~~~~~~~~~~~~~~~~ computeSubstitutionCounts.h:53:13: warning: ‘int computeSubstitutionCounts::_simulationsIterNum’ [-Wreorder] 53 | int _simulationsIterNum; | ^~~~~~~~~~~~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): | ^~~~~~~~~~~~~~~~~~~~~~~~~ computeSubstitutionCounts.h:54:17: warning: ‘computeSubstitutionCounts::_probCutOffSum’ will be initialized after [-Wreorder] 54 | MDOUBLE _probCutOffSum; | ^~~~~~~~~~~~~~ computeSubstitutionCounts.h:52:14: warning: ‘bool computeSubstitutionCounts::_isSilent’ [-Wreorder] 52 | bool _isSilent; | ^~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): | ^~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp In file included from /usr/aarch64-linux-gnu/include/c++/12/iostream:39, from readTree.h:6, from tree.h:7, from computeDownAlg.h:7, from computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:2: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:72:3: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’: computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:35: note: ‘pij’ was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:72:3: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’: computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:31: note: ‘Up’ was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:72:3: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’: computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:25: note: ‘Down’ was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3, inlined from ‘virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function ‘virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)’: computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:35: note: ‘pij’ was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3, inlined from ‘virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function ‘virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)’: computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:31: note: ‘Up’ was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3, inlined from ‘virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp: In member function ‘virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)’: computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:55:25: note: ‘Down’ was declared here 55 | MDOUBLE resDXY, Down, Up, pij; | ^~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp In file included from fromCountTableComponentToDistancePropEB.cpp:3: fromCountTableComponentToDistancePropEB.h: In constructor ‘fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector >&, int, multipleStochasticProcess*, const gammaDistribution*, double, double)’: fromCountTableComponentToDistancePropEB.h:29:19: warning: ‘fromCountTableComponentToDistancePropEB::_nodeID’ will be initialized after [-Wreorder] 29 | const int _nodeID; | ^~~~~~~ fromCountTableComponentToDistancePropEB.h:28:34: warning: ‘const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist’ [-Wreorder] 28 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp goldmanYangModel.cpp: In constructor ‘goldmanYangModel::goldmanYangModel(double, double, codon&, bool)’: goldmanYangModel.cpp:8:1: warning: ‘goldmanYangModel::_globalV’ is initialized with itself [-Winit-self] 8 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): | ^~~~~~~~~~~~~~~~ goldmanYangModel.cpp: In constructor ‘goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)’: goldmanYangModel.cpp:18:1: warning: ‘goldmanYangModel::_globalV’ is initialized with itself [-Winit-self] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp likeDist.cpp: In instantiation of ‘double myNRmethod(double, double, double, regF, dF, double, int, int&) [with regF = C_evalLikeDist_d; dF = C_evalLikeDist_d2]’: likeDist.cpp:269:22: required from here likeDist.cpp:210:13: warning: variable ‘oldIntervalSize’ set but not used [-Wunused-but-set-variable] 210 | MDOUBLE oldIntervalSize = currentIntervalSize; | ^~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp In file included from /usr/aarch64-linux-gnu/include/c++/12/cassert:44, from njConstrain.cpp:4: njConstrain.cpp: In function ‘tree::TreeNode* joinNodesToSubtree(tree&, tree::TreeNode*&, tree::TreeNode*&)’: njConstrain.cpp:92:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 92 | assert (k=fatherNode->getNumberOfSons()+2); // both s1 and s2 should have been skiped | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] 306 | //* for (i=1;i>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp sequence.cpp: In constructor ‘sequence::sequence(const sequence&, const alphabet*)’: sequence.cpp:76:42: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 76 | || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp sequenceContainer.cpp: In member function ‘void sequenceContainer::removeGapPositions()’: sequenceContainer.cpp:187:14: warning: variable ‘gapCol’ set but not used [-Wunused-but-set-variable] 187 | bool gapCol; | ^~~~~~ sequenceContainer.cpp: In member function ‘void sequenceContainer::removeGapPositionsAllSeqs()’: sequenceContainer.cpp:199:14: warning: variable ‘gapCol’ set but not used [-Wunused-but-set-variable] 199 | bool gapCol; | ^~~~~~ sequenceContainer.cpp: In member function ‘int sequenceContainer::getNumOfOccurancesPerPos(int, char)’: sequenceContainer.cpp:452:19: warning: unused variable ‘len’ [-Wunused-variable] 452 | const int len = _seqDataVec[0].seqLen(); | ^~~ sequenceContainer.cpp: In member function ‘std::vector > sequenceContainer::getSeqNamesThatMatchPos(int, char)’: sequenceContainer.cpp:467:19: warning: unused variable ‘len’ [-Wunused-variable] 467 | const int len = _seqDataVec[0].seqLen(); | ^~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp tree.cpp: In constructor ‘tree::tree(const std::string&)’: tree.cpp:180:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if (in.is_open()) | ^~ tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 182 | create_names_to_internal_nodes(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp treeUtil.cpp: In function ‘std::vector getNexusTreesFromFile(const std::string&)’: treeUtil.cpp:371:32: warning: variable ‘itStrStart’ set but not used [-Wunused-but-set-variable] 371 | string::const_iterator itStrStart = it->begin(); | ^~~~~~~~~~ treeUtil.cpp:372:32: warning: variable ‘itStrEnd’ set but not used [-Wunused-but-set-variable] 372 | string::const_iterator itStrEnd = it->end(); | ^~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp In file included from distanceBasedSeqs2Tree.cpp:12: bestGtrModelParams.h: In constructor ‘C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)’: bestGtrModelParams.h:175:28: warning: ‘C_evalGTRParamProportional::_sp’ will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ bestGtrModelParams.h:173:34: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp In file included from betaDistribution.cpp:3: betaDistribution.h: In copy constructor ‘betaDistribution::betaDistribution(const betaDistribution&)’: betaDistribution.h:54:25: warning: ‘betaDistribution::_boundary’ will be initialized after [-Wreorder] 54 | vector _boundary; | ^~~~~~~~~ betaDistribution.h:47:17: warning: ‘double betaDistribution::_alpha’ [-Wreorder] 47 | MDOUBLE _alpha; | ^~~~~~ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] 23 | betaDistribution::betaDistribution(const betaDistribution& other) : | ^~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp In file included from computeJumps.cpp:1: computeJumps.h: In constructor ‘computeJumps::gFunc::gFunc(double, double, double)’: computeJumps.h:59:25: warning: ‘computeJumps::gFunc::_Lambda2’ will be initialized after [-Wreorder] 59 | MDOUBLE _Lambda2; | ^~~~~~~~ computeJumps.h:57:25: warning: ‘double computeJumps::gFunc::_r’ [-Wreorder] 57 | MDOUBLE _r; | ^~ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) | ^~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp seqeuncesFilter.cpp: In static member function ‘static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)’: seqeuncesFilter.cpp:141:25: warning: unused variable ‘pAlph’ [-Wunused-variable] 141 | const alphabet* pAlph = sc.getAlphabet(); | ^~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/12/vector:64, from definitions.h:18, from seqeuncesFilter.h:5, from seqeuncesFilter.cpp:1: In member function ‘std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = int; _Alloc = std::allocator]’, inlined from ‘const sequence& sequenceContainer::operator[](int) const’ at sequenceContainer.h:31:81, inlined from ‘static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)’ at seqeuncesFilter.cpp:175:16: /usr/aarch64-linux-gnu/include/c++/12/bits/stl_vector.h:1143:41: warning: ‘refID’ may be used uninitialized [-Wmaybe-uninitialized] 1143 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ seqeuncesFilter.cpp: In static member function ‘static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)’: seqeuncesFilter.cpp:165:13: note: ‘refID’ was declared here 165 | int refID; | ^~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp In file included from /usr/aarch64-linux-gnu/include/c++/12/vector:64, from definitions.h:18, from mixtureDistribution.h:11, from mixtureDistribution.cpp:1: In member function ‘std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]’, inlined from ‘virtual const double mixtureDistribution::rates(int) const’ at mixtureDistribution.cpp:221:33: /usr/aarch64-linux-gnu/include/c++/12/bits/stl_vector.h:1143:41: warning: ‘componentNum’ may be used uninitialized [-Wmaybe-uninitialized] 1143 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mixtureDistribution.cpp: In member function ‘virtual const double mixtureDistribution::rates(int) const’: mixtureDistribution.cpp:210:13: note: ‘componentNum’ was declared here 210 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘virtual const double generalGammaDistribution::rates(int) const’ at generalGammaDistribution.h:27:65, inlined from ‘virtual const double mixtureDistribution::rates(int) const’ at mixtureDistribution.cpp:221:41: /usr/aarch64-linux-gnu/include/c++/12/bits/stl_vector.h:1143:41: warning: ‘categoryInComponent’ may be used uninitialized [-Wmaybe-uninitialized] 1143 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mixtureDistribution.cpp: In member function ‘virtual const double mixtureDistribution::rates(int) const’: mixtureDistribution.cpp:210:27: note: ‘categoryInComponent’ was declared here 210 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘const double mixtureDistribution::getComponentProb(int) const’ at mixtureDistribution.h:40:95, inlined from ‘virtual const double mixtureDistribution::ratesProb(int) const’ at mixtureDistribution.cpp:239:26: /usr/aarch64-linux-gnu/include/c++/12/bits/stl_vector.h:1143:41: warning: ‘componentNum’ may be used uninitialized [-Wmaybe-uninitialized] 1143 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mixtureDistribution.cpp: In member function ‘virtual const double mixtureDistribution::ratesProb(int) const’: mixtureDistribution.cpp:228:13: note: ‘componentNum’ was declared here 228 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~ In member function ‘std::vector<_Tp, _Alloc>::const_reference std::vector<_Tp, _Alloc>::operator[](size_type) const [with _Tp = double; _Alloc = std::allocator]’, inlined from ‘virtual const double generalGammaDistribution::ratesProb(int) const’ at generalGammaDistribution.h:28:73, inlined from ‘virtual const double mixtureDistribution::ratesProb(int) const’ at mixtureDistribution.cpp:239:79: /usr/aarch64-linux-gnu/include/c++/12/bits/stl_vector.h:1143:41: warning: ‘categoryInComponent’ may be used uninitialized [-Wmaybe-uninitialized] 1143 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ mixtureDistribution.cpp: In member function ‘virtual const double mixtureDistribution::ratesProb(int) const’: mixtureDistribution.cpp:228:27: note: ‘categoryInComponent’ was declared here 228 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp suffStatGammaMixture.cpp: In member function ‘void suffStatGammaMixture::computeStatistics()’: suffStatGammaMixture.cpp:123:33: warning: variable ‘Exp_Rk’ set but not used [-Wunused-but-set-variable] 123 | MDOUBLE Exp_Rk, Exp_LogRk, sum; | ^~~~~~ suffStatGammaMixture.cpp: In member function ‘double suffStatGammaMixture::computeQ()’: suffStatGammaMixture.cpp:224:25: warning: unused variable ‘first’ [-Wunused-variable] 224 | MDOUBLE first = _MkVec[comp] * log(P_k); | ^~~~~ suffStatGammaMixture.cpp:225:25: warning: unused variable ‘second’ [-Wunused-variable] 225 | MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); | ^~~~~~ suffStatGammaMixture.cpp:226:25: warning: unused variable ‘third’ [-Wunused-variable] 226 | MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); | ^~~~~ suffStatGammaMixture.cpp:227:25: warning: unused variable ‘fourth’ [-Wunused-variable] 227 | MDOUBLE fourth = -_AkVec[comp]*beta_k; | ^~~~~~ suffStatGammaMixture.cpp:228:25: warning: unused variable ‘fifth’ [-Wunused-variable] 228 | MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); | ^~~~~ suffStatGammaMixture.cpp:216:17: warning: variable ‘res2’ set but not used [-Wunused-but-set-variable] 216 | MDOUBLE res2 = 0.0; | ^~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp In file included from GamMixtureOptimizer.cpp:3: optGammaMixtureEM.h: In member function ‘double C_evalAlphaEM::diGammaPlus(double) const’: optGammaMixtureEM.h:76:25: warning: unused variable ‘res1’ [-Wunused-variable] 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); | ^~~~ optGammaMixtureEM.h: In member function ‘double C_evalAlphaEM::diGamma(double) const’: optGammaMixtureEM.h:87:25: warning: unused variable ‘debugRes’ [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp In file included from optGammaMixtureEM.cpp:1: optGammaMixtureEM.h: In member function ‘double C_evalAlphaEM::diGammaPlus(double) const’: optGammaMixtureEM.h:76:25: warning: unused variable ‘res1’ [-Wunused-variable] 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); | ^~~~ optGammaMixtureEM.h: In member function ‘double C_evalAlphaEM::diGamma(double) const’: optGammaMixtureEM.h:87:25: warning: unused variable ‘debugRes’ [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp In file included from gtrModel.cpp:1: gtrModel.h: In constructor ‘gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)’: gtrModel.h:54:17: warning: ‘gtrModel::_g2t’ will be initialized after [-Wreorder] 54 | MDOUBLE _g2t; | ^~~~ gtrModel.h:47:17: warning: ‘Vdouble gtrModel::_freq’ [-Wreorder] 47 | Vdouble _freq; | ^~~~~ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] 5 | gtrModel::gtrModel(const Vdouble& freq, | ^~~~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_a2c() const’: gtrModel.cpp:139:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 139 | return result; | ^~~~~~ gtrModel.cpp:130:17: note: ‘result’ was declared here 130 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_a2g() const’: gtrModel.cpp:153:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 153 | return result; | ^~~~~~ gtrModel.cpp:144:17: note: ‘result’ was declared here 144 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_a2t() const’: gtrModel.cpp:167:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 167 | return result; | ^~~~~~ gtrModel.cpp:158:17: note: ‘result’ was declared here 158 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_c2g() const’: gtrModel.cpp:181:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 181 | return result; | ^~~~~~ gtrModel.cpp:172:17: note: ‘result’ was declared here 172 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_c2t() const’: gtrModel.cpp:195:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 195 | return result; | ^~~~~~ gtrModel.cpp:186:17: note: ‘result’ was declared here 186 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_g2t() const’: gtrModel.cpp:209:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 209 | return result; | ^~~~~~ gtrModel.cpp:200:17: note: ‘result’ was declared here 200 | MDOUBLE result; | ^~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp In file included from bestGtrModelParams.cpp:3: bestGtrModelParams.h: In constructor ‘C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)’: bestGtrModelParams.h:175:28: warning: ‘C_evalGTRParamProportional::_sp’ will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ bestGtrModelParams.h:173:34: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp ar rv libEvolTree.a AddLog.o NNiProp.o NNiSep.o Nni.o aaJC.o allTrees.o allTreesSeparateModel.o alphabet.o amino.o bestAlpha.o bestAlphaManyTrees.o bestHKYparam.o bootstrap.o bblEM.o bblEMfixRoot.o bblEMProprtional.o bblEMProportionalEB.o bblLSProportionalEB.o bblEMSeperate.o chebyshevAccelerator.o clustalFormat.o codon.o codonJC.o computeCounts.o computeDownAlg.o computeMarginalAlg.o computePijComponent.o computeUpAlg.o computeUpAlgFactors.o computeSubstitutionCounts.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o ConversionUtils.o countTableComponent.o datMatrixHolder.o distanceTable.o distribution.o errorMsg.o evaluateCharacterFreq.o fastStartTree.o fastaFormat.o findRateOfGene.o fromCountTableComponentToDistance.o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistancePropEB.o fromQtoPt.o generalGammaDistributionFixedCategories.o gammaDistribution.o gammaUtilities.o generalGammaDistribution.o getRandomWeights.o goldmanYangModel.o granthamChemicalDistances.o hky.o simulateWithDependence.o KH_calculation.o likeDist.o likeDistfixRoot.o likeDistProp.o likeDistPropEB.o likelihoodComputation.o likelihoodComputationFactors.o logFile.o maseFormat.o molphyFormat.o nexusFormat.o nj.o njConstrain.o nucJC.o nucleotide.o numRec.o Parameters.o phylipFormat.o pijAccelerator.o readDatMatrix.o readTree.o recognizeFormat.o replacementModel.o searchStatus.o seqContainerTreeMap.o sequence.o sequenceContainer.o simulateTree.o siteSpecificRate.o someUtil.o split.o splitMap.o splitTreeUtil.o stochasticProcess.o suffStatComponent.o talRandom.o tree.o treeIt.o treeUtil.o uniDistribution.o uniformDistribution.o cmdline2EvolObjs.o generalGammaDistributionLaguerre.o gammaDistributionLaguerre.o GLaguer.o givenRatesMLDistance.o distanceBasedSeqs2Tree.o posteriorDistance.o pairwiseGammaDistance.o doubleRep.o logRep.o indel.o indelModel.o mulAlphabet.o replacementModelSSRV.o stochasticProcessSSRV.o bestAlphaAndNu.o C_evalParamUSSRV.o matrixUtils.o betaOmegaDistribution.o betaUtilities.o betaDistribution.o geneticCodeHolder.o samplingSequences.o bblEM2USSRV.o bestParamUSSRV.o likeDist2USSRV.o ussrvModel.o likelihoodComputation2USSRV.o fromCountTableComponentToDistance2USSRV.o normalDist.o tamura92.o bestTamura92param.o phylipSequentialFormat.o simulateCodonsJumps.o simulateJumpsAbstract.o ssrvDistanceSeqs2Tree.o multipleStochasticProcess.o distributionPlusInvariant.o extremeValDistribution.o gammaDistributionFixedCategories.o generalGammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.o distributionPlusCategory.o simulateJumps.o computeJumps.o seqeuncesFilter.o optGammaMixtureLS.o mixtureDistribution.o suffStatGammaMixture.o GamMixtureOptimizer.o optGammaMixtureEM.o gainLossAlphabet.o wYangModel.o codonUtils.o likelihoodComputation2Codon.o likeDist2Codon.o unObservableData.o likelihoodComputationGL.o threeStateModel.o threeStateAlphabet.o oneTwoMoreModel.o betaDistributionFixedCategories.o betaDistributionFixedCategoriesWithOmegaUniform.o bblEM2codon.o bestAlphaAndK.o fromCountTableComponentToDistance2Codon.o gtrModel.o bestGtrModelParams.o simulateRateShiftJumps.o integerAlphabet.o ar: creating libEvolTree.a a - AddLog.o a - NNiProp.o a - NNiSep.o a - Nni.o a - aaJC.o a - allTrees.o a - allTreesSeparateModel.o a - alphabet.o a - amino.o a - bestAlpha.o a - bestAlphaManyTrees.o a - bestHKYparam.o a - bootstrap.o a - bblEM.o a - bblEMfixRoot.o a - bblEMProprtional.o a - bblEMProportionalEB.o a - bblLSProportionalEB.o a - bblEMSeperate.o a - chebyshevAccelerator.o a - clustalFormat.o a - codon.o a - codonJC.o a - computeCounts.o a - computeDownAlg.o a - computeMarginalAlg.o a - computePijComponent.o a - computeUpAlg.o a - computeUpAlgFactors.o a - computeSubstitutionCounts.o a - computePosteriorExpectationOfSubstitutions.o a - computePosteriorExpectationOfSubstitutions_nonReversibleSp.o a - ConversionUtils.o a - countTableComponent.o a - datMatrixHolder.o a - distanceTable.o a - distribution.o a - errorMsg.o a - evaluateCharacterFreq.o a - fastStartTree.o a - fastaFormat.o a - findRateOfGene.o a - fromCountTableComponentToDistance.o a - fromCountTableComponentToDistancefixRoot.o a - fromCountTableComponentToDistanceProp.o a - fromCountTableComponentToDistancePropEB.o a - fromQtoPt.o a - generalGammaDistributionFixedCategories.o a - gammaDistribution.o a - gammaUtilities.o a - generalGammaDistribution.o a - getRandomWeights.o a - goldmanYangModel.o a - granthamChemicalDistances.o a - hky.o a - simulateWithDependence.o a - KH_calculation.o a - likeDist.o a - likeDistfixRoot.o a - likeDistProp.o a - likeDistPropEB.o a - likelihoodComputation.o a - likelihoodComputationFactors.o a - logFile.o a - maseFormat.o a - molphyFormat.o a - nexusFormat.o a - nj.o a - njConstrain.o a - nucJC.o a - nucleotide.o a - numRec.o a - Parameters.o a - phylipFormat.o a - pijAccelerator.o a - readDatMatrix.o a - readTree.o a - recognizeFormat.o a - replacementModel.o a - searchStatus.o a - seqContainerTreeMap.o a - sequence.o a - sequenceContainer.o a - simulateTree.o a - siteSpecificRate.o a - someUtil.o a - split.o a - splitMap.o a - splitTreeUtil.o a - stochasticProcess.o a - suffStatComponent.o a - talRandom.o a - tree.o a - treeIt.o a - treeUtil.o a - uniDistribution.o a - uniformDistribution.o a - cmdline2EvolObjs.o a - generalGammaDistributionLaguerre.o a - gammaDistributionLaguerre.o a - GLaguer.o a - givenRatesMLDistance.o a - distanceBasedSeqs2Tree.o a - posteriorDistance.o a - pairwiseGammaDistance.o a - doubleRep.o a - logRep.o a - indel.o a - indelModel.o a - mulAlphabet.o a - replacementModelSSRV.o a - stochasticProcessSSRV.o a - bestAlphaAndNu.o a - C_evalParamUSSRV.o a - matrixUtils.o a - betaOmegaDistribution.o a - betaUtilities.o a - betaDistribution.o a - geneticCodeHolder.o a - samplingSequences.o a - bblEM2USSRV.o a - bestParamUSSRV.o a - likeDist2USSRV.o a - ussrvModel.o a - likelihoodComputation2USSRV.o a - fromCountTableComponentToDistance2USSRV.o a - normalDist.o a - tamura92.o a - bestTamura92param.o a - phylipSequentialFormat.o a - simulateCodonsJumps.o a - simulateJumpsAbstract.o a - ssrvDistanceSeqs2Tree.o a - multipleStochasticProcess.o a - distributionPlusInvariant.o a - extremeValDistribution.o a - gammaDistributionFixedCategories.o a - generalGammaDistributionPlusInvariant.o a - gammaDistributionPlusInvariant.o a - distributionPlusCategory.o a - simulateJumps.o a - computeJumps.o a - seqeuncesFilter.o a - optGammaMixtureLS.o a - mixtureDistribution.o a - suffStatGammaMixture.o a - GamMixtureOptimizer.o a - optGammaMixtureEM.o a - gainLossAlphabet.o a - wYangModel.o a - codonUtils.o a - likelihoodComputation2Codon.o a - likeDist2Codon.o a - unObservableData.o a - likelihoodComputationGL.o a - threeStateModel.o a - threeStateAlphabet.o a - oneTwoMoreModel.o a - betaDistributionFixedCategories.o a - betaDistributionFixedCategoriesWithOmegaUniform.o a - bblEM2codon.o a - bestAlphaAndK.o a - fromCountTableComponentToDistance2Codon.o a - gtrModel.o a - bestGtrModelParams.o a - simulateRateShiftJumps.o a - integerAlphabet.o ranlib libEvolTree.a make[3]: Leaving directory '/<>/libs/phylogeny' make[2]: Leaving directory '/<>/libs' cd programs;make all make[2]: Entering directory '/<>/programs' cd fastml && make all make[3]: Entering directory '/<>/programs/fastml' making depend aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp In file included from bbAlg.h:8, from fastml.cpp:254: bbReport.h: In constructor ‘BandBReportAllPos::BandBReportAllPos(const std::string&, int)’: bbReport.h:14:23: warning: ‘BandBReportAllPos::_reportFileName’ will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ In file included from mainbb.h:4, from fastml.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor ‘BandBReportAllPos::BandBReportAllPos(const std::string&, int)’: bbReport.h:14:23: warning: ‘BandBReportAllPos::_reportFileName’ will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ bbAlg.h: In constructor ‘bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, boundMethod, const std::string&, double, const distribution*)’: bbAlg.h:61:23: warning: ‘bbAlg::_reportFileName’ will be initialized after [-Wreorder] 61 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbAlg.h:60:27: warning: ‘BandBReportAllPos bbAlg::BandBReportAllPos1’ [-Wreorder] 60 | BandBReportAllPos BandBReportAllPos1; // report for all positions. | ^~~~~~~~~~~~~~~~~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(const tree& et, | ^~~~~ bbAlg.h:60:27: warning: ‘bbAlg::BandBReportAllPos1’ will be initialized after [-Wreorder] 60 | BandBReportAllPos BandBReportAllPos1; // report for all positions. | ^~~~~~~~~~~~~~~~~~ bbAlg.h:29:21: warning: ‘const tree& bbAlg::_et’ [-Wreorder] 29 | const tree& _et; | ^~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(const tree& et, | ^~~~~ In file included from bbNodeOrderAlg.h:5, from bbAlg.h:5: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp In file included from bbEvaluateSpecificAV.cpp:1: bbEvaluateSpecificAV.h: In constructor ‘bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)’: bbEvaluateSpecificAV.h:34:34: warning: ‘bbEvaluateSpecificAV::_sc’ will be initialized after [-Wreorder] 34 | const sequenceContainer& _sc; | ^~~ bbEvaluateSpecificAV.h:31:30: warning: ‘const computePijGam& bbEvaluateSpecificAV::_bbcpij’ [-Wreorder] 31 | const computePijGam& _bbcpij; | ^~~~~~~ bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] 3 | bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, | ^~~~~~~~~~~~~~~~~~~~ bbEvaluateSpecificAV.cpp: In member function ‘double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)’: bbEvaluateSpecificAV.cpp:65:33: warning: unused variable ‘rate’ [-Wunused-variable] 65 | MDOUBLE rate = _sp.rates(categor); // the r. | ^~~~ In file included from bbEvaluateSpecificAV.h:4: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp In file included from bbfindBestAVDynProg.h:5, from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp In file included from bbNodeOrderAlg.cpp:1: bbNodeOrderAlg.h: In constructor ‘bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)’: bbNodeOrderAlg.h:33:34: warning: ‘bbNodeOrderAlg::_sc’ will be initialized after [-Wreorder] 33 | const sequenceContainer& _sc; | ^~~ bbNodeOrderAlg.h:32:30: warning: ‘const computePijGam& bbNodeOrderAlg::_cpij’ [-Wreorder] 32 | const computePijGam& _cpij; | ^~~~~ bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] 8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, | ^~~~~~~~~~~~~~ In file included from bbNodeOrderAlg.h:5: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp In file included from bb_options.cpp:2: bb_options.h: In constructor ‘bb_options::bb_options(int&, char**)’: bb_options.h:49:16: warning: ‘bb_options::reportFile’ will be initialized after [-Wreorder] 49 | string reportFile; | ^~~~~~~~~~ bb_options.h:44:16: warning: ‘std::string bb_options::outFile_seq_joint’ [-Wreorder] 44 | string outFile_seq_joint; | ^~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:45:16: warning: ‘bb_options::outFile_seq_marginal’ will be initialized after [-Wreorder] 45 | string outFile_seq_marginal; | ^~~~~~~~~~~~~~~~~~~~ bb_options.h:42:16: warning: ‘std::string bb_options::outFile_prob_joint’ [-Wreorder] 42 | string outFile_prob_joint; | ^~~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:43:16: warning: ‘bb_options::outFile_prob_marginal’ will be initialized after [-Wreorder] 43 | string outFile_prob_marginal; | ^~~~~~~~~~~~~~~~~~~~~ bb_options.h:24:16: warning: ‘std::string bb_options::seqfile’ [-Wreorder] 24 | string seqfile; | ^~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:30:28: warning: ‘bb_options::distributionName’ will be initialized after [-Wreorder] 30 | distributionsNames distributionName; | ^~~~~~~~~~~~~~~~ bb_options.h:26:23: warning: ‘bb_options::SeqFileFormat bb_options::seqOutputFormat’ [-Wreorder] 26 | SeqFileFormat seqOutputFormat; | ^~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:41:16: warning: ‘bb_options::outTreeFileAncestor’ will be initialized after [-Wreorder] 41 | string outTreeFileAncestor; | ^~~~~~~~~~~~~~~~~~~ bb_options.h:32:22: warning: ‘bb_options::boundMethods bb_options::boundMethod’ [-Wreorder] 32 | boundMethods boundMethod; | ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:47:17: warning: ‘bb_options::gammaPar’ will be initialized after [-Wreorder] 47 | MDOUBLE gammaPar; | ^~~~~~~~ bb_options.h:28:14: warning: ‘bool bb_options::userProvideAlpha’ [-Wreorder] 28 | bool userProvideAlpha; | ^~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:48:13: warning: ‘bb_options::gammaCategies’ will be initialized after [-Wreorder] 48 | int gammaCategies; | ^~~~~~~~~~~~~ bb_options.h:36:26: warning: ‘bb_options::modelNameOptions bb_options::modelName’ [-Wreorder] 36 | modelNameOptions modelName; | ^~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:39:14: warning: ‘bb_options::useChebyshev’ will be initialized after [-Wreorder] 39 | bool useChebyshev; | ^~~~~~~~~~~~ bb_options.h:27:16: warning: ‘std::string bb_options::treeOutFile’ [-Wreorder] 27 | string treeOutFile; | ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp In file included from bbReport.cpp:1: bbReport.h: In constructor ‘BandBReportAllPos::BandBReportAllPos(const std::string&, int)’: bbReport.h:14:23: warning: ‘BandBReportAllPos::_reportFileName’ will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ bbReport.h: In constructor ‘BandBReport::BandBReport(const std::string&, int, int)’: bbReport.h:53:23: warning: ‘BandBReport::_reportFileName’ will be initialized after [-Wreorder] 53 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:51:19: warning: ‘const int BandBReport::_position’ [-Wreorder] 51 | const int _position; | ^~~~~~~~~ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : | ^~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp computeMarginalReconstruction.cpp: In member function ‘void computeMarginalReconstruction::compute(const distribution*)’: computeMarginalReconstruction.cpp:67:25: warning: unused variable ‘likelihoodOfPos’ [-Wunused-variable] 67 | MDOUBLE likelihoodOfPos = 0; | ^~~~~~~~~~~~~~~ computeMarginalReconstruction.cpp:45:17: warning: unused variable ‘totalLikelihoodOfReconstruction’ [-Wunused-variable] 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp jointNoGamma.cpp: In member function ‘void jointNoGamma::compute()’: jointNoGamma.cpp:23:17: warning: unused variable ‘totalLikelihoodOfReconstruction’ [-Wunused-variable] 23 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jointNoGamma.cpp: In member function ‘std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)’: jointNoGamma.cpp:108:33: warning: unused variable ‘maxL’ [-Wunused-variable] 108 | MDOUBLE maxL = VERYSMALL; | ^~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp In file included from bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor ‘BandBReportAllPos::BandBReportAllPos(const std::string&, int)’: bbReport.h:14:23: warning: ‘BandBReportAllPos::_reportFileName’ will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h: In constructor ‘C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)’: ../../libs/phylogeny/bestGtrModelParams.h:175:28: warning: ‘C_evalGTRParamProportional::_sp’ will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ ../../libs/phylogeny/bestGtrModelParams.h:173:34: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mainbb.h:4, from mainbb.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ mainbb.cpp: In member function ‘void mainbb::findAncestralSequencesGammaJoint()’: mainbb.cpp:428:108: warning: ‘bm’ may be used uninitialized [-Wmaybe-uninitialized] 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); | ^ mainbb.cpp:423:28: note: ‘bm’ was declared here 423 | bbAlg::boundMethod bm; | ^~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o ar: creating libfastml.a a - fastml.o a - bbAlg.o a - bbComputeDownAlg.o a - bbComputeUpAlg.o a - bbEvaluateSpecificAV.o a - bbfindBestAVDynProg.o a - bbNodeOrderAlg.o a - bb_options.o a - bbReport.o a - computeMarginalReconstruction.o a - jointNoGamma.o a - mainbb.o a - sequenceDataDiff.o a - suffStatComponentJointNoGamma.o ranlib libfastml.a aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml make[3]: Leaving directory '/<>/programs/fastml' cd gainLoss && make all make[3]: Entering directory '/<>/programs/gainLoss' making depend aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp gainLossOptions.cpp: In static member function ‘static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)’: gainLossOptions.cpp:2064:16: warning: ‘returnType’ may be used uninitialized [-Wmaybe-uninitialized] 2064 | return returnType; | ^~~~~~~~~~ gainLossOptions.cpp:2047:27: note: ‘returnType’ was declared here 2047 | optimizationLevel returnType; | ^~~~~~~~~~ gainLossOptions.cpp: In static member function ‘static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)’: gainLossOptions.cpp:2111:16: warning: ‘returnType’ may be used uninitialized [-Wmaybe-uninitialized] 2111 | return returnType; | ^~~~~~~~~~ gainLossOptions.cpp:2098:24: note: ‘returnType’ was declared here 2098 | costMatrixType returnType; | ^~~~~~~~~~ gainLossOptions.cpp: In static member function ‘static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)’: gainLossOptions.cpp:2419:16: warning: ‘returnType’ may be used uninitialized [-Wmaybe-uninitialized] 2419 | return returnType; | ^~~~~~~~~~ gainLossOptions.cpp:2396:24: note: ‘returnType’ was declared here 2396 | simulationType returnType; | ^~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp In file included from gainLoss.h:35, from gainLoss.cpp:20: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.cpp:41: bblLS.h: At global scope: bblLS.h:50:31: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:31: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 58 | MDOUBLE curL =NULL); | ^~~~ bblLS.h: In constructor ‘evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)’: bblLS.h:119:27: warning: ‘evalBranchSPvv::_unObservableData_p’ will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:18: warning: ‘Vdouble* evalBranchSPvv::_weights’ [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:18: warning: when initialized here [-Wreorder] 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~ bblLS.h: In constructor ‘evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)’: bblLS.h:174:27: warning: ‘evalBranchProportionExponentSPvv::_unObservableData_p’ will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:18: warning: ‘Vdouble* evalBranchProportionExponentSPvv::_weights’ [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.h: In constructor ‘gainLoss::gainLoss()’: gainLoss.h:266:28: warning: ‘gainLoss::_unObservableData_p’ will be initialized after [-Wreorder] 266 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLoss.h:240:23: warning: ‘distribution* gainLoss::_lossDist’ [-Wreorder] 240 | distribution* _lossDist; | ^~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 63 | gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) | ^~~~~~~~ gainLoss.h:240:23: warning: ‘gainLoss::_lossDist’ will be initialized after [-Wreorder] 240 | distribution* _lossDist; | ^~~~~~~~~ gainLoss.h:239:23: warning: ‘distribution* gainLoss::_gainDist’ [-Wreorder] 239 | distribution* _gainDist; | ^~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 63 | gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) | ^~~~~~~~ gainLoss.h:273:19: warning: ‘gainLoss::_refSeq’ will be initialized after [-Wreorder] 273 | sequence* _refSeq; // the reference sequence | ^~~~~~~ gainLoss.h:267:18: warning: ‘Vdouble* gainLoss::_weightsUniqPatterns’ [-Wreorder] 267 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:63:1: warning: when initialized here [-Wreorder] 63 | gainLoss::gainLoss(): _sp(NULL),_unObservableData_p(NULL),_lossDist(NULL), _gainDist(NULL), _refSeq(NULL), _weightsUniqPatterns(NULL) | ^~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::removePositionsWithHighPercentOfMissingData(double)’: gainLoss.cpp:604:14: warning: unused variable ‘missigDataChar’ [-Wunused-variable] 604 | char missigDataChar = -2; | ^~~~~~~~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::startEvolTreeTopology(std::ostream&)’: gainLoss.cpp:1245:64: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ | ^~ gainLoss.cpp:1245:45: note: add parentheses around left hand side expression to silence this warning 1245 | if(gainLossOptions::_seqFile!="" && !_tr.getLeavesNum()==_sc.numberOfSeqs()){ | ^~~~~~~~~~~~~~~~~~~ | ( ) gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’: gainLoss.cpp:1868:25: warning: unused variable ‘sumPijQij’ [-Wunused-variable] 1868 | MDOUBLE sumPijQij = normalizeQ(sp); | ^~~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1990:25: warning: unused variable ‘sumPijQij’ [-Wunused-variable] 1990 | MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist); | ^~~~~~~~~ gainLoss.cpp: In member function ‘double gainLoss::computeDistanceFromRootForRecent(tree&)’: gainLoss.cpp:4205:14: warning: variable ‘isRecentBiggerAncient’ set but not used [-Wunused-but-set-variable] 4205 | bool isRecentBiggerAncient = true; | ^~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function ‘double gainLoss::computeDistanceNearestOTUforRecent(tree&)’: gainLoss.cpp:4283:14: warning: variable ‘isRecentBiggerAncient’ set but not used [-Wunused-but-set-variable] 4283 | bool isRecentBiggerAncient = true; | ^~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::multipleAllBranchesByFactorAtStart(double)’: gainLoss.cpp:4382:40: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ | ^ gainLoss.cpp:4382:28: note: add parentheses around left hand side expression to silence this warning 4382 | if(! currBestL > _logL+epsilonOptimization && isStopAfterNoImprovment){ | ^~~~~~~~~~~ | ( ) gainLoss.cpp: In member function ‘void gainLoss::startSimultePosteriorExpectationOfChange(int, int)’: gainLoss.cpp:4951:33: warning: variable ‘sumQii’ set but not used [-Wunused-but-set-variable] 4951 | MDOUBLE sumQii = 1.0; | ^~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/12/iostream:39, from ../../libs/phylogeny/readTree.h:6, from ../../libs/phylogeny/tree.h:7, from ../../libs/phylogeny/simulateJumpsAbstract.h:5, from ../../libs/phylogeny/simulateJumps.h:4, from computePosteriorExpectationOfChange.h:24, from gainLoss.cpp:19: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’ at gainLoss.cpp:1877:25: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currBeta’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’: gainLoss.cpp:1844:17: note: ‘currBeta’ was declared here 1844 | MDOUBLE currBeta; | ^~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’ at gainLoss.cpp:1876:26: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currAlpha’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’: gainLoss.cpp:1843:17: note: ‘currAlpha’ was declared here 1843 | MDOUBLE currAlpha; | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’ at gainLoss.cpp:1875:40: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currM2’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’: gainLoss.cpp:1842:17: note: ‘currM2’ was declared here 1842 | MDOUBLE currM2; | ^~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’ at gainLoss.cpp:2005:17: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currTheta’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1946:17: note: ‘currTheta’ was declared here 1946 | MDOUBLE currTheta; | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’ at gainLoss.cpp:2004:21: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currAlpha’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1945:17: note: ‘currAlpha’ was declared here 1945 | MDOUBLE currAlpha; //Rate | ^~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’ at gainLoss.cpp:2002:22: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currLossProbInvariant’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1944:17: note: ‘currLossProbInvariant’ was declared here 1944 | MDOUBLE currLossProbInvariant; | ^~~~~~~~~~~~~~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’ at gainLoss.cpp:2001:25: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currLossBeta’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1943:17: note: ‘currLossBeta’ was declared here 1943 | MDOUBLE currLossBeta; | ^~~~~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’ at gainLoss.cpp:2000:4: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currLossAlpha’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1942:17: note: ‘currLossAlpha’ was declared here 1942 | MDOUBLE currLossAlpha; // Loss (for non-reversible model only) | ^~~~~~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’ at gainLoss.cpp:1998:21: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘currGainProbInvariant’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1941:17: note: ‘currGainProbInvariant’ was declared here 1941 | MDOUBLE currGainProbInvariant; | ^~~~~~~~~~~~~~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’ at gainLoss.cpp:2044:2: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘bestGainBeta’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1929:17: note: ‘bestGainBeta’ was declared here 1929 | MDOUBLE bestGainBeta=1; | ^~~~~~~~~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’ at gainLoss.cpp:3897:53: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘Theta’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’: gainLoss.cpp:3852:37: note: ‘Theta’ was declared here 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; | ^~~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’ at gainLoss.cpp:3897:41: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘Loss’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’: gainLoss.cpp:3852:32: note: ‘Loss’ was declared here 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; | ^~~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’ at gainLoss.cpp:3897:12: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘AlphaRate’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ gainLoss.cpp: In member function ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’: gainLoss.cpp:3852:17: note: ‘AlphaRate’ was declared here 3852 | MDOUBLE AlphaRate,Gain,Loss,Theta; | ^~~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()’: gainLoss.cpp:3980:73: warning: ‘AlphaLoss’ may be used uninitialized [-Wmaybe-uninitialized] 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); | ~~~~~~~~~~^~~~~~~~~~~ gainLoss.cpp:3947:27: note: ‘AlphaLoss’ was declared here 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; | ^~~~~~~~~ gainLoss.cpp:3980:73: warning: ‘AlphaGain’ may be used uninitialized [-Wmaybe-uninitialized] 3980 | gainLossRatioToCompleteByBeta = ratio*(AlphaLoss/AlphaGain); | ~~~~~~~~~~^~~~~~~~~~~ gainLoss.cpp:3947:17: note: ‘AlphaGain’ was declared here 3947 | MDOUBLE AlphaGain,AlphaLoss, BetaGain,BetaLoss, gainLossRatioToCompleteByBeta, ratio =1; | ^~~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::startStochasticProcess()’: gainLoss.cpp:869:30: warning: ‘rateDist’ may be used uninitialized [-Wmaybe-uninitialized] 869 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted | ^~~~~~~~ gainLoss.cpp:806:23: note: ‘rateDist’ was declared here 806 | distribution* rateDist; | ^~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::startStochasticProcessVec()’: gainLoss.cpp:1127:46: warning: ‘rateDist’ may be used uninitialized [-Wmaybe-uninitialized] 1127 | if (rateDist) delete rateDist; //at r4s after the sp object is created all other objects dynamically constructed are deleted | ^~~~~~~~ gainLoss.cpp:1105:39: note: ‘rateDist’ was declared here 1105 | distribution* rateDist; | ^~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)’: gainLoss.cpp:2511:29: warning: ‘countsGL’ may be used uninitialized [-Wmaybe-uninitialized] 2511 | if(countsGL) delete countsGL; | ^~~~~~~~ gainLoss.cpp:2466:26: note: ‘countsGL’ was declared here 2466 | computeCountsGL* countsGL; | ^~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::startEvolTreeTopology(std::ostream&)’: gainLoss.cpp:1195:24: warning: ‘pDm’ may be used uninitialized [-Wmaybe-uninitialized] 1195 | delete pDm; | ^~~ gainLoss.cpp:1173:33: note: ‘pDm’ was declared here 1173 | distanceMethod* pDm; | ^~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp In file included from gainLossUtils.cpp:19: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossUtils.cpp: In function ‘void printTreeWithValuesAsBP(std::ostream&, tree::TreeNode* const&, Vstring, VVVdouble*, bool)’: gainLossUtils.cpp:72:19: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 72 | if(probs) | ^ gainLossUtils.cpp:88:27: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 88 | if(probs) | ^ gainLossUtils.cpp: In function ‘void updateGainBeta(double, std::vector >&, distribution*, distribution*, bool)’: gainLossUtils.cpp:481:17: warning: variable ‘normFactor’ set but not used [-Wunused-but-set-variable] 481 | MDOUBLE normFactor; | ^~~~~~~~~~ gainLossUtils.cpp: In function ‘double sumPijQijVec(std::vector >&, distribution*, distribution*)’: gainLossUtils.cpp:788:17: warning: unused variable ‘scale’ [-Wunused-variable] 788 | MDOUBLE scale; | ^~~~~ gainLossUtils.cpp: In function ‘double getRateBeta(distribution*)’: gainLossUtils.cpp:312:16: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 312 | return res; | ^~~ gainLossUtils.cpp:285:17: note: ‘res’ was declared here 285 | MDOUBLE res; | ^~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.h: In constructor ‘optimizeGainLossModel::optimizeGainLossModel(const tree&, stochasticProcess&, const sequenceContainer&, bool, double, int, Vdouble*, unObservableData*)’: optimizeGainLossModel.h:87:18: warning: ‘optimizeGainLossModel::_weightsUniqPatterns’ will be initialized after [-Wreorder] 87 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.h:86:27: warning: ‘unObservableData* optimizeGainLossModel::_unObservableData_p’ [-Wreorder] 86 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:20:1: warning: when initialized here [-Wreorder] 20 | optimizeGainLossModel::optimizeGainLossModel(const tree& tr, stochasticProcess& sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModel.cpp:85:17: warning: variable ‘sumPijQij’ set but not used [-Wunused-but-set-variable] 85 | MDOUBLE sumPijQij; | ^~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from optimizeGainLossModelVV.h:27, from optimizeGainLossModelVV.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.h: In constructor ‘optimizeGainLossModelVV::optimizeGainLossModelVV(const tree&, std::vector >&, const sequenceContainer&, distribution*, distribution*, bool, double, int, Vdouble*, unObservableData*)’: optimizeGainLossModelVV.h:82:18: warning: ‘optimizeGainLossModelVV::_weightsUniqPatterns’ will be initialized after [-Wreorder] 82 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.h:81:27: warning: ‘unObservableData* optimizeGainLossModelVV::_unObservableData_p’ [-Wreorder] 81 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:25:1: warning: when initialized here [-Wreorder] 25 | optimizeGainLossModelVV::optimizeGainLossModelVV(const tree& tr, | ^~~~~~~~~~~~~~~~~~~~~~~ optimizeGainLossModelVV.cpp:258:41: warning: unused variable ‘currentlogL’ [-Wunused-variable] 258 | MDOUBLE currentlogL = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(tr,sc,spVVec,gainDist,lossDist,_weightsUniqPatterns,_unObservableData_p); | ^~~~~~~~~~~ optimizeGainLossModelVV.cpp:76:17: warning: variable ‘sumPijQij’ set but not used [-Wunused-but-set-variable] 76 | MDOUBLE sumPijQij; | ^~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp In file included from gainLossModel.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h: In constructor ‘gainLossModel::gainLossModel(double, Vdouble, bool, bool, bool, bool)’: gainLossModel.h:108:17: warning: ‘gainLossModel::_gain’ will be initialized after [-Wreorder] 108 | MDOUBLE _gain; // _Q[0][1] | ^~~~~ gainLossModel.h:105:17: warning: ‘Vdouble gainLossModel::_freq’ [-Wreorder] 105 | Vdouble _freq; | ^~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): | ^~~~~~~~~~~~~ gainLossModel.h:112:14: warning: ‘gainLossModel::_isRootFreqEQstationary’ will be initialized after [-Wreorder] 112 | bool _isRootFreqEQstationary; | ^~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:111:14: warning: ‘bool gainLossModel::_isReversible’ [-Wreorder] 111 | bool _isReversible; | ^~~~~~~~~~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): | ^~~~~~~~~~~~~ gainLossModel.h:114:14: warning: ‘gainLossModel::_isHGT_with_Q’ will be initialized after [-Wreorder] 114 | bool _isHGT_with_Q; | ^~~~~~~~~~~~~ gainLossModel.h:110:15: warning: ‘q2pt* gainLossModel::_q2pt’ [-Wreorder] 110 | q2pt *_q2pt; // dont use q2p | ^~~~~ gainLossModel.cpp:24:1: warning: when initialized here [-Wreorder] 24 | gainLossModel::gainLossModel(const MDOUBLE m1, const Vdouble freq, bool isRootFreqEQstationary, bool isReversible, bool isHGT_normal_Pij, bool isHGT_with_Q): | ^~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp In file included from siteSpecificGL.cpp:24: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp In file included from computePosteriorExpectationOfChange.cpp:25: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/12/iostream:39, from ../../libs/phylogeny/readTree.h:6, from ../../libs/phylogeny/tree.h:7, from ../../libs/phylogeny/simulateJumpsAbstract.h:5, from ../../libs/phylogeny/simulateJumps.h:4, from computePosteriorExpectationOfChange.h:24, from computePosteriorExpectationOfChange.cpp:17: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’ at computePosteriorExpectationOfChange.cpp:233:3: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfChange.cpp: In member function ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’: computePosteriorExpectationOfChange.cpp:216:17: note: ‘pij’ was declared here 216 | MDOUBLE pij; | ^~~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’ at computePosteriorExpectationOfChange.cpp:233:3: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfChange.cpp: In member function ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’: computePosteriorExpectationOfChange.cpp:215:33: note: ‘Up’ was declared here 215 | doubleRep resDXY, Down, Up; | ^~ In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(double) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’ at computePosteriorExpectationOfChange.cpp:233:3: /usr/aarch64-linux-gnu/include/c++/12/ostream:221:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 221 | { return _M_insert(__f); } | ~~~~~~~~~^~~~~ computePosteriorExpectationOfChange.cpp: In member function ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’: computePosteriorExpectationOfChange.cpp:215:27: note: ‘Down’ was declared here 215 | doubleRep resDXY, Down, Up; | ^~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from gainLoss.h:35, from gainLossProject.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from gainLoss.h:35, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLossOptimizer.cpp:20: bblLS.h: At global scope: bblLS.h:50:31: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:31: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 58 | MDOUBLE curL =NULL); | ^~~~ bblLS.h: In constructor ‘evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)’: bblLS.h:119:27: warning: ‘evalBranchSPvv::_unObservableData_p’ will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:18: warning: ‘Vdouble* evalBranchSPvv::_weights’ [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:18: warning: when initialized here [-Wreorder] 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~ bblLS.h: In constructor ‘evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)’: bblLS.h:174:27: warning: ‘evalBranchProportionExponentSPvv::_unObservableData_p’ will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:18: warning: ‘Vdouble* evalBranchProportionExponentSPvv::_weights’ [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h: In constructor ‘gainLossOptimizer::gainLossOptimizer(tree&, stochasticProcess*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)’: gainLossOptimizer.h:134:14: warning: ‘gainLossOptimizer::_tr’ will be initialized after [-Wreorder] 134 | tree _tr; | ^~~ gainLossOptimizer.h:109:28: warning: ‘stochasticProcess* gainLossOptimizer::_sp’ [-Wreorder] 109 | stochasticProcess *_sp; | ^~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h:135:27: warning: ‘gainLossOptimizer::_sc’ will be initialized after [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.h:93:17: warning: ‘double gainLossOptimizer::_epsilonOptimization’ [-Wreorder] 93 | MDOUBLE _epsilonOptimization; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h:104:18: warning: ‘gainLossOptimizer::_weightsUniqPatterns’ will be initialized after [-Wreorder] 104 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:28: warning: ‘unObservableData* gainLossOptimizer::_unObservableData_p’ [-Wreorder] 102 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:25:1: warning: when initialized here [-Wreorder] 25 | gainLossOptimizer::gainLossOptimizer(tree& tr, stochasticProcess* sp, const sequenceContainer &sc, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h: In constructor ‘gainLossOptimizer::gainLossOptimizer(tree&, std::vector >&, distribution*, distribution*, const sequenceContainer&, double, int, double, int, double, int, Vdouble*, unObservableData*, bool, bool)’: gainLossOptimizer.h:139:23: warning: ‘gainLossOptimizer::_lossDist’ will be initialized after [-Wreorder] 139 | distribution* _lossDist; | ^~~~~~~~~ gainLossOptimizer.h:135:27: warning: ‘sequenceContainer gainLossOptimizer::_sc’ [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h:135:27: warning: ‘gainLossOptimizer::_sc’ will be initialized after [-Wreorder] 135 | sequenceContainer _sc; | ^~~ gainLossOptimizer.h:93:17: warning: ‘double gainLossOptimizer::_epsilonOptimization’ [-Wreorder] 93 | MDOUBLE _epsilonOptimization; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.h:104:18: warning: ‘gainLossOptimizer::_weightsUniqPatterns’ will be initialized after [-Wreorder] 104 | Vdouble* _weightsUniqPatterns; | ^~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.h:102:28: warning: ‘unObservableData* gainLossOptimizer::_unObservableData_p’ [-Wreorder] 102 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:50:1: warning: when initialized here [-Wreorder] 50 | gainLossOptimizer::gainLossOptimizer(tree& tr, vector >& spVVec, distribution * gainDist, distribution * lossDist, | ^~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp: In member function ‘double gainLossOptimizer::optimizeBranchLengths(int)’: gainLossOptimizer.cpp:498:33: warning: unused variable ‘oldLnoUnObservableDataCorrection’ [-Wunused-variable] 498 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:543:33: warning: unused variable ‘oldLnoUnObservableDataCorrection’ [-Wunused-variable] 543 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,*_sp,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:487:17: warning: variable ‘newLnoUnObservableDataCorrection’ set but not used [-Wunused-but-set-variable] 487 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp: In member function ‘double gainLossOptimizer::optimizeBranchLengthsvv(int)’: gainLossOptimizer.cpp:634:33: warning: unused variable ‘oldLnoUnObservableDataCorrection’ [-Wunused-variable] 634 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:677:33: warning: unused variable ‘oldLnoUnObservableDataCorrection’ [-Wunused-variable] 677 | MDOUBLE oldLnoUnObservableDataCorrection = likelihoodComputationGL::getTreeLikelihoodAllPosAlphTheSame(_tr,_sc,_spVVec,_gainDist,_lossDist,_weightsUniqPatterns,NULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp:623:17: warning: variable ‘newLnoUnObservableDataCorrection’ set but not used [-Wunused-but-set-variable] 623 | MDOUBLE newLnoUnObservableDataCorrection = VERYSMALL; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossOptimizer.cpp: In function ‘gainLossOptions::distributionType getRateDistributionType(distribution*)’: gainLossOptimizer.cpp:833:16: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 833 | return res; | ^~~ gainLossOptimizer.cpp:820:43: note: ‘res’ was declared here 820 | gainLossOptions::distributionType res; | ^~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp In file included from gainLoss.h:35, from rate4siteGL.h:24, from rate4siteGL.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ rate4siteGL.h: In constructor ‘rate4siteGL::rate4siteGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, unObservableData*)’: rate4siteGL.h:59:14: warning: ‘rate4siteGL::_tr’ will be initialized after [-Wreorder] 59 | tree _tr; | ^~~ rate4siteGL.h:58:28: warning: ‘stochasticProcess* rate4siteGL::_sp’ [-Wreorder] 58 | stochasticProcess *_sp; | ^~~ rate4siteGL.cpp:24:1: warning: when initialized here [-Wreorder] 24 | rate4siteGL::rate4siteGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, unObservableData* unObservableData_p): | ^~~~~~~~~~~ rate4siteGL.cpp: In member function ‘void rate4siteGL::printRatesBayes(std::ostream&, const Vdouble&)’: rate4siteGL.cpp:151:13: warning: unused variable ‘precisionHigh’ [-Wunused-variable] 151 | int precisionHigh = 5; | ^~~~~~~~~~~~~ rate4siteGL.cpp:152:13: warning: unused variable ‘precisionLow’ [-Wunused-variable] 152 | int precisionLow = 3; | ^~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp In file included from gainLoss.h:35, from computeCountsGL.h:24, from computeCountsGL.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h: In constructor ‘computeCountsGL::computeCountsGL(sequenceContainer&, tree&, stochasticProcess*, std::string&, VVdouble&, double, bool)’: computeCountsGL.h:104:14: warning: ‘computeCountsGL::_tr’ will be initialized after [-Wreorder] 104 | tree _tr; | ^~~ computeCountsGL.h:102:28: warning: ‘stochasticProcess* computeCountsGL::_sp’ [-Wreorder] 102 | stochasticProcess *_sp; | ^~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 28 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ computeCountsGL.h:117:17: warning: ‘computeCountsGL::_distanceFromNearestOTUForRecent’ will be initialized after [-Wreorder] 117 | MDOUBLE _distanceFromNearestOTUForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:14: warning: ‘bool computeCountsGL::_isSilent’ [-Wreorder] 113 | bool _isSilent; | ^~~~~~~~~ computeCountsGL.cpp:28:1: warning: when initialized here [-Wreorder] 28 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, stochasticProcess* sp, string& outDir, VVdouble& logLpostPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ computeCountsGL.h: In constructor ‘computeCountsGL::computeCountsGL(sequenceContainer&, tree&, std::vector >&, distribution*, distribution*, std::string&, VVVdouble&, double, bool)’: computeCountsGL.h:109:23: warning: ‘computeCountsGL::_lossDist’ will be initialized after [-Wreorder] 109 | distribution* _lossDist; | ^~~~~~~~~ computeCountsGL.h:105:27: warning: ‘sequenceContainer computeCountsGL::_sc’ [-Wreorder] 105 | sequenceContainer _sc; | ^~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ computeCountsGL.h:117:17: warning: ‘computeCountsGL::_distanceFromNearestOTUForRecent’ will be initialized after [-Wreorder] 117 | MDOUBLE _distanceFromNearestOTUForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCountsGL.h:113:14: warning: ‘bool computeCountsGL::_isSilent’ [-Wreorder] 113 | bool _isSilent; | ^~~~~~~~~ computeCountsGL.cpp:33:1: warning: when initialized here [-Wreorder] 33 | computeCountsGL::computeCountsGL(sequenceContainer& sc, tree& tr, vector >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent): | ^~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp In file included from gainLoss.h:35, from computeCorrelations.h:25, from computeCorrelations.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)’: computeCorrelations.cpp:130:13: warning: unused variable ‘numOfbranches’ [-Wunused-variable] 130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node | ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)’: computeCorrelations.cpp:408:29: warning: unused variable ‘isHigherNminReducedFreqOfHighCorr’ [-Wunused-variable] 408 | int isHigherNminReducedFreqOfHighCorr = false; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:348:21: warning: unused variable ‘typeIndex’ [-Wunused-variable] 348 | int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used | ^~~~~~~~~ computeCorrelations.cpp: In member function ‘void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)’: computeCorrelations.cpp:559:30: warning: NULL used in arithmetic [-Wpointer-arith] 559 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:569:38: warning: NULL used in arithmetic [-Wpointer-arith] 569 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:579:38: warning: NULL used in arithmetic [-Wpointer-arith] 579 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:584:30: warning: NULL used in arithmetic [-Wpointer-arith] 584 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp: In member function ‘int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)’: computeCorrelations.cpp:676:37: warning: variable ‘prevNumberOfSimulationsInRange’ set but not used [-Wunused-but-set-variable] 676 | int prevNumberOfSimulationsInRange = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:677:37: warning: variable ‘prevNumberOfSimulationPointsMoreExtremeOrEqToCorr’ set but not used [-Wunused-but-set-variable] 677 | int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:679:37: warning: unused variable ‘numOfBinsWithLowerSignificance’ [-Wunused-variable] 679 | int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:680:38: warning: unused variable ‘isNextLowerBinAllowed’ [-Wunused-variable] 680 | bool isNextLowerBinAllowed = true; | ^~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)’: computeCorrelations.cpp:894:26: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 894 | if(!numOfSites_A == numOfSites_B){ | ^~ computeCorrelations.cpp:894:12: note: add parentheses around left hand side expression to silence this warning 894 | if(!numOfSites_A == numOfSites_B){ | ^~~~~~~~~~~~~ | ( ) computeCorrelations.cpp: In member function ‘void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::string*)’: computeCorrelations.cpp:1009:14: warning: unused variable ‘isPearson’ [-Wunused-variable] 1009 | bool isPearson = false; | ^~~~~~~~~ computeCorrelations.cpp:1025:13: warning: unused variable ‘numOfbranches’ [-Wunused-variable] 1025 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node | ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)’: computeCorrelations.cpp:1347:67: warning: narrowing conversion of ‘gainLossOptions::_pValueCutOffForBootStrap’ from ‘double’ to ‘float’ [-Wnarrowing] 1347 | float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:1300:14: warning: variable ‘it_siteB’ set but not used [-Wunused-but-set-variable] 1300 | it_B it_siteB = it_siteA->second.begin(); | ^~~~~~~~ computeCorrelations.cpp: In member function ‘int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)’: computeCorrelations.cpp:505:33: warning: ‘expextedFreq’ may be used uninitialized [-Wmaybe-uninitialized] 505 | if(freqOfHighCorr>expextedFreq && freqOfHighCorr>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp In file included from gainLoss.h:35, from gainLoss4site.h:24, from gainLoss4site.cpp:17: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss4site.h: In constructor ‘gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)’: gainLoss4site.h:68:14: warning: ‘gainLoss4site::_tr’ will be initialized after [-Wreorder] 68 | tree _tr; | ^~~ gainLoss4site.h:61:45: warning: ‘std::vector > gainLoss4site::_spVVec’ [-Wreorder] 61 | vector > _spVVec; //save stochasticProcess for each category | ^~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ gainLoss4site.h:79:27: warning: ‘gainLoss4site::_unObservableData_p’ will be initialized after [-Wreorder] 79 | unObservableData* _unObservableData_p; // | ^~~~~~~~~~~~~~~~~~~ gainLoss4site.h:78:17: warning: ‘double gainLoss4site::_alphaConf’ [-Wreorder] 78 | MDOUBLE _alphaConf; | ^~~~~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from gainLoss.h:35, from simulateChangesAlongTree.cpp:20: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp In file included from gainLoss.h:35, from simulateOnePos.cpp:32: gainLossModel.h: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h: In constructor ‘simulateOnePos::simulateOnePos(std::string, std::ostream*, std::ostream*, int, std::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)’: simulateOnePos.h:72:14: warning: ‘simulateOnePos::_simulateNullModel’ will be initialized after [-Wreorder] 72 | bool _simulateNullModel; | ^~~~~~~~~~~~~~~~~~ simulateOnePos.h:63:13: warning: ‘int simulateOnePos::_simNum’ [-Wreorder] 63 | int _simNum; | ^~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.h:65:17: warning: ‘simulateOnePos::_theta’ will be initialized after [-Wreorder] 65 | MDOUBLE _theta; | ^~~~~~ simulateOnePos.h:64:17: warning: ‘double simulateOnePos::_sumGainLoss’ [-Wreorder] 64 | MDOUBLE _sumGainLoss; | ^~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.h:75:18: warning: ‘simulateOnePos::_freq_cpN’ will be initialized after [-Wreorder] 75 | Vdouble* _freq_cpN; | ^~~~~~~~~ simulateOnePos.h:69:18: warning: ‘std::ostream* simulateOnePos::_simulatedEvents’ [-Wreorder] 69 | ostream *_simulatedEvents; | ^~~~~~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.cpp: In member function ‘void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)’: simulateOnePos.cpp:181:30: warning: unused variable ‘isRevers’ [-Wunused-variable] 181 | bool isRevers = false; | ^~~~~~~~ simulateOnePos.cpp:202:33: warning: variable ‘sumQii’ set but not used [-Wunused-but-set-variable] 202 | MDOUBLE sumQii = 1.0; | ^~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp In file included from bblLS.cpp:17: bblLS.h:50:31: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:31: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 58 | MDOUBLE curL =NULL); | ^~~~ bblLS.h: In constructor ‘evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)’: bblLS.h:119:27: warning: ‘evalBranchSPvv::_unObservableData_p’ will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:18: warning: ‘Vdouble* evalBranchSPvv::_weights’ [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:18: warning: when initialized here [-Wreorder] 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~ bblLS.h: In constructor ‘evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)’: bblLS.h:174:27: warning: ‘evalBranchProportionExponentSPvv::_unObservableData_p’ will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:18: warning: ‘Vdouble* evalBranchProportionExponentSPvv::_weights’ [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bblLS.cpp: In member function ‘double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)’: bblLS.cpp:36:21: warning: NULL used in arithmetic [-Wpointer-arith] 36 | if (curL == NULL) | ^~~~ bblLS.cpp: In member function ‘double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)’: bblLS.cpp:112:21: warning: NULL used in arithmetic [-Wpointer-arith] 112 | if (curL == NULL) | ^~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from sankoffReconstructGL.cpp:17: sankoffReconstructGL.h: In constructor ‘sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)’: sankoffReconstructGL.h:85:16: warning: ‘sankoffReconstructGL::_outDir’ will be initialized after [-Wreorder] 85 | string _outDir; | ^~~~~~~ sankoffReconstructGL.h:84:17: warning: ‘double sankoffReconstructGL::_costMatrixGainLossRatio’ [-Wreorder] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:84:17: warning: ‘sankoffReconstructGL::_costMatrixGainLossRatio’ will be initialized after [-Wreorder] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:83:17: warning: ‘double sankoffReconstructGL::_distanceFromRootForRecent’ [-Wreorder] 83 | MDOUBLE _distanceFromRootForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ ar rv libgainLoss.a gainLossOptions.o gainLoss.o gainLossUtils.o optimizeGainLossModel.o optimizeGainLossModelVV.o ../../libs/phylogeny/likelihoodComputationGL.o gainLossModel.o siteSpecificGL.o computePosteriorExpectationOfChange.o gainLossProject.o gainLossOptimizer.o ancestralReconstructStates.o rate4siteGL.o computeCountsGL.o computeCorrelations.o gainLoss4site.o simulateChangesAlongTree.o simulateOnePos.o bblLS.o sankoffReconstructGL.o ar: creating libgainLoss.a a - gainLossOptions.o a - gainLoss.o a - gainLossUtils.o a - optimizeGainLossModel.o a - optimizeGainLossModelVV.o a - ../../libs/phylogeny/likelihoodComputationGL.o a - gainLossModel.o a - siteSpecificGL.o a - computePosteriorExpectationOfChange.o a - gainLossProject.o a - gainLossOptimizer.o a - ancestralReconstructStates.o a - rate4siteGL.o a - computeCountsGL.o a - computeCorrelations.o a - gainLoss4site.o a - simulateChangesAlongTree.o a - simulateOnePos.o a - bblLS.o a - sankoffReconstructGL.o ranlib libgainLoss.a aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss make[3]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make all make[3]: Entering directory '/<>/programs/indelCoder' making depend aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp indelCoder.cpp: In member function ‘void indelCoder::printGapsInfo()’: indelCoder.cpp:422:13: warning: unused variable ‘gapNum’ [-Wunused-variable] 422 | int gapNum = 1; | ^~~~~~ indelCoder.cpp: In member function ‘void indelCoder::printIndelSummary()’: indelCoder.cpp:587:14: warning: unused variable ‘isSIC’ [-Wunused-variable] 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; | ^~~~~ indelCoder.cpp:597:13: warning: unused variable ‘seqLeng’ [-Wunused-variable] 597 | int seqLeng = _sc.seqLen(); | ^~~~~~~ indelCoder.cpp: In member function ‘void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)’: indelCoder.cpp:175:33: warning: ‘condition’ may be used uninitialized [-Wmaybe-uninitialized] 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indelCoder.cpp:170:22: note: ‘condition’ was declared here 170 | bool condition; | ^~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp character.cpp: In member function ‘int character::getLongestGapStIndex()’: character.cpp:28:16: warning: ‘longestGapStIndex’ may be used uninitialized [-Wmaybe-uninitialized] 28 | return longestGapStIndex; | ^~~~~~~~~~~~~~~~~ character.cpp:17:13: note: ‘longestGapStIndex’ was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/12/vector:64, from ../../libs/phylogeny/definitions.h:18, from character.h:4, from character.cpp:1: In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator[](size_type) [with _Tp = int; _Alloc = std::allocator]’, inlined from ‘void character::checkForTriangleInequality(int, int)’ at character.cpp:6:63: /usr/aarch64-linux-gnu/include/c++/12/bits/stl_vector.h:1124:41: warning: ‘longestGapStIndex’ may be used uninitialized [-Wmaybe-uninitialized] 1124 | return *(this->_M_impl._M_start + __n); | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ character.cpp: In member function ‘void character::checkForTriangleInequality(int, int)’: character.cpp:17:13: note: ‘longestGapStIndex’ was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ aarch64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a a - indelCoder.o a - indelCoderOptions.o a - indelCoderProject.o a - indelCoderUtils.o a - character.o a - gaps.o ranlib libindelCoder.a aarch64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder make[3]: Leaving directory '/<>/programs/indelCoder' make[2]: Leaving directory '/<>/programs' make[1]: Leaving directory '/<>' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/fastml/ -a make -j1 install DESTDIR=/<>/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/libs/phylogeny' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/libs/phylogeny' make[2]: Leaving directory '/<>/libs' cd programs;make install make[2]: Entering directory '/<>/programs' cd fastml && make install make[3]: Entering directory '/<>/programs/fastml' mkdir -p ../../bin cp fastml ../../bin/fastml make[3]: Leaving directory '/<>/programs/fastml' cd gainLoss && make install make[3]: Entering directory '/<>/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make install make[3]: Entering directory '/<>/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder make[3]: Leaving directory '/<>/programs/indelCoder' make[2]: Leaving directory '/<>/programs' make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'fastml' in '../fastml_3.11-3_arm64.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-3_arm64.deb'. dpkg-genbuildinfo --build=any -O../fastml_3.11-3_arm64.buildinfo dpkg-genchanges --build=any -O../fastml_3.11-3_arm64.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2022-12-19T01:56:10Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ fastml_3.11-3_arm64.changes: ---------------------------- Format: 1.8 Date: Thu, 17 Dec 2020 15:31:13 +0100 Source: fastml Binary: fastml fastml-dbgsym Built-For-Profiles: cross nocheck Architecture: arm64 Version: 3.11-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fastml - maximum likelihood ancestral amino-acid sequence reconstruction Changes: fastml (3.11-3) unstable; urgency=medium . * Standards-Version: 4.5.1 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * watch file standard 4 (routine-update) Checksums-Sha1: 2b2a97e14d5b886f6cbcf416175671c8713c9a7b 18705900 fastml-dbgsym_3.11-3_arm64.deb 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+------------------------------------------------------------------------------+ Format: 1.0 Source: fastml Binary: fastml fastml-dbgsym Architecture: arm64 Version: 3.11-3 Checksums-Md5: 991bf23f04befef0b9474e3efcd71989 18705900 fastml-dbgsym_3.11-3_arm64.deb 80d55b279d54723839ecf92ead0d6395 787080 fastml_3.11-3_arm64.deb Checksums-Sha1: 2b2a97e14d5b886f6cbcf416175671c8713c9a7b 18705900 fastml-dbgsym_3.11-3_arm64.deb 9982f9293fb1ea2d2527ac4b2bf632d6668eaf62 787080 fastml_3.11-3_arm64.deb Checksums-Sha256: b7c8867a748e01b2f748f954b290326e22f9acd8c775bc2287648da5466bee87 18705900 fastml-dbgsym_3.11-3_arm64.deb 4794ae5e9e175d035a7382bea301072abad5a83468fee64ba37ab750ac1419d3 787080 fastml_3.11-3_arm64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 19 Dec 2022 01:56:09 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-2), automake (= 1:1.16.5-1.3), autopoint (= 0.21-10), autotools-dev (= 20220109.1), base-files (= 12.3), base-passwd (= 3.6.1), bash (= 5.2-2+b1), binutils (= 2.39.50.20221208-5), binutils-common (= 2.39.50.20221208-5), binutils-x86-64-linux-gnu (= 2.39.50.20221208-5), bsdextrautils (= 2.38.1-4), bsdutils (= 1:2.38.1-4), build-essential (= 12.9), bzip2 (= 1.0.8-5+b1), coreutils (= 9.1-1), cpp (= 4:12.2.0-1), cpp-11 (= 11.3.0-8), cpp-12 (= 12.2.0-10), dash (= 0.5.11+git20210903+057cd650a4ed-9), debconf (= 1.5.80), debhelper (= 13.11.3), debianutils (= 5.7-0.4), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.0-2), diffutils (= 1:3.8-2), dpkg (= 1.21.12), dpkg-dev (= 1.21.12), dwz (= 0.14+20220924-2), file (= 1:5.41-4), findutils (= 4.9.0-3), g++ (= 4:12.2.0-1), g++-12 (= 12.2.0-10), gcc (= 4:12.2.0-1), gcc-11 (= 11.3.0-8), gcc-11-base (= 11.3.0-8), gcc-12 (= 12.2.0-10), gcc-12-base (= 12.2.0-10), gettext (= 0.21-10), gettext-base (= 0.21-10), grep (= 3.8-3), groff-base (= 1.22.4-9), gzip (= 1.12-1), hostname (= 3.23), init-system-helpers (= 1.65.2), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.1-2), libarchive-zip-perl (= 1.68-1), libasan6 (= 11.3.0-8), libasan8 (= 12.2.0-10), libatomic1 (= 12.2.0-10), libattr1 (= 1:2.5.1-3), libaudit-common (= 1:3.0.7-1.1), libaudit1 (= 1:3.0.7-1.1+b2), libbinutils (= 2.39.50.20221208-5), libblkid1 (= 2.38.1-4), libbz2-1.0 (= 1.0.8-5+b1), libc-bin (= 2.36-6), libc-dev-bin (= 2.36-6), libc6 (= 2.36-6), libc6-dev (= 2.36-6), libcap-ng0 (= 0.8.3-1+b2), libcap2 (= 1:2.66-2), libcc1-0 (= 12.2.0-10), libcom-err2 (= 1.46.6~rc1-1+b1), libcrypt-dev (= 1:4.4.33-1), libcrypt1 (= 1:4.4.33-1), libctf-nobfd0 (= 2.39.50.20221208-5), libctf0 (= 2.39.50.20221208-5), libdb5.3 (= 5.3.28+dfsg1-0.10), libdebconfclient0 (= 0.265), libdebhelper-perl (= 13.11.3), libdpkg-perl (= 1.21.12), libelf1 (= 0.188-1), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.0-2), libgcc-11-dev (= 11.3.0-8), libgcc-12-dev (= 12.2.0-10), libgcc-s1 (= 12.2.0-10), libgcrypt20 (= 1.10.1-3), libgdbm-compat4 (= 1.23-3), libgdbm6 (= 1.23-3), libgmp10 (= 2:6.2.1+dfsg1-1.1), libgomp1 (= 12.2.0-10), libgpg-error0 (= 1.46-1), libgprofng0 (= 2.39.50.20221208-5), libgssapi-krb5-2 (= 1.20.1-1), libicu72 (= 72.1-3), libisl23 (= 0.25-1), libitm1 (= 12.2.0-10), libjansson4 (= 2.14-2), libk5crypto3 (= 1.20.1-1), libkeyutils1 (= 1.6.3-1), libkrb5-3 (= 1.20.1-1), libkrb5support0 (= 1.20.1-1), liblsan0 (= 12.2.0-10), liblz4-1 (= 1.9.4-1), liblzma5 (= 5.4.0-0.1), libmagic-mgc (= 1:5.41-4), libmagic1 (= 1:5.41-4), libmd0 (= 1.0.4-2), libmount1 (= 2.38.1-4), libmpc3 (= 1.2.1-2), libmpfr6 (= 4.1.0-3), libnsl-dev (= 1.3.0-2), libnsl2 (= 1.3.0-2), libnumber-compare-perl (= 0.03-3), libpam-modules (= 1.5.2-5), libpam-modules-bin (= 1.5.2-5), libpam-runtime (= 1.5.2-5), libpam0g (= 1.5.2-5), libpcre2-8-0 (= 10.40-3), libperl5.36 (= 5.36.0-6), libpipeline1 (= 1.5.7-1), libquadmath0 (= 12.2.0-10), libseccomp2 (= 2.5.4-1+b2), libselinux1 (= 3.4-1+b3), libsmartcols1 (= 2.38.1-4), libssl3 (= 3.0.7-1), libstdc++-12-dev (= 12.2.0-10), libstdc++6 (= 12.2.0-10), libsub-override-perl (= 0.09-4), libsystemd0 (= 252.3-2), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.3+20220423-2), libtirpc-common (= 1.3.3+ds-1), libtirpc-dev (= 1.3.3+ds-1), libtirpc3 (= 1.3.3+ds-1), libtool (= 2.4.7-5), libtsan0 (= 11.3.0-8), libtsan2 (= 12.2.0-10), libubsan1 (= 12.2.0-10), libuchardet0 (= 0.0.7-1), libudev1 (= 252.3-2), libunistring2 (= 1.0-2), libuuid1 (= 2.38.1-4), libxml2 (= 2.9.14+dfsg-1.1+b2), libzstd1 (= 1.5.2+dfsg-1), linux-libc-dev (= 6.0.12-1), login (= 1:4.13+dfsg1-1), m4 (= 1.4.19-1), make (= 4.3-4.1), man-db (= 2.11.1-1), mawk (= 1.3.4.20200120-3.1), ncurses-base (= 6.3+20220423-2), ncurses-bin (= 6.3+20220423-2), patch (= 2.7.6-7), perl (= 5.36.0-6), perl-base (= 5.36.0-6), perl-modules-5.36 (= 5.36.0-6), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.8-1), sensible-utils (= 0.0.17), sysvinit-utils (= 3.05-7), tar (= 1.34+dfsg-1.1), usrmerge (= 35), util-linux (= 2.38.1-4), util-linux-extra (= 2.38.1-4), xz-utils (= 5.4.0-0.1), zlib1g (= 1:1.2.13.dfsg-1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1608215473" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ fastml-dbgsym_3.11-3_arm64.deb ------------------------------ new Debian package, version 2.0. size 18705900 bytes: control archive=700 bytes. 448 bytes, 12 lines control 402 bytes, 4 lines md5sums Package: fastml-dbgsym Source: fastml Version: 3.11-3 Auto-Built-Package: debug-symbols Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 18767 Depends: fastml (= 3.11-3) Section: debug Priority: optional Description: debug symbols for fastml Build-Ids: 06e4b34a7d4a9995651b30f344342e400540d4b5 5103a5dde5e956d233f832030b8ff6b41bcaa2c9 ed43d3db6595ef14472a97c2f492679ca488b6cf drwxr-xr-x root/root 0 2020-12-17 14:31 ./ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/lib/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/lib/debug/.build-id/06/ -rw-r--r-- root/root 6628168 2020-12-17 14:31 ./usr/lib/debug/.build-id/06/e4b34a7d4a9995651b30f344342e400540d4b5.debug drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/lib/debug/.build-id/51/ -rw-r--r-- root/root 9998128 2020-12-17 14:31 ./usr/lib/debug/.build-id/51/03a5dde5e956d233f832030b8ff6b41bcaa2c9.debug drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/lib/debug/.build-id/ed/ -rw-r--r-- root/root 1352264 2020-12-17 14:31 ./usr/lib/debug/.build-id/ed/43d3db6595ef14472a97c2f492679ca488b6cf.debug drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/lib/debug/.dwz/aarch64-linux-gnu/ -rw-r--r-- root/root 1223296 2020-12-17 14:31 ./usr/lib/debug/.dwz/aarch64-linux-gnu/fastml.debug drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/share/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-12-17 14:31 ./usr/share/doc/fastml-dbgsym -> fastml fastml_3.11-3_arm64.deb ----------------------- new Debian package, version 2.0. size 787080 bytes: control archive=1236 bytes. 1432 bytes, 26 lines control 494 bytes, 8 lines md5sums Package: fastml Version: 3.11-3 Architecture: arm64 Maintainer: Debian Med Packaging Team Installed-Size: 3098 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11) Section: science Priority: optional Homepage: http://fastml.tau.ac.il/ Description: maximum likelihood ancestral amino-acid sequence reconstruction FastML is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences. FastML runs several algorithms that reconstruct the ancestral sequences with emphasis on an accurate reconstruction of both indels and characters. For character reconstruction the previously described FastML algorithms are used to efficiently infer the most likely ancestral sequences for each internal node of the tree. Both joint and the marginal reconstructions are provided. For indels reconstruction the sequences are first coded according to the indel events detected within the multiple sequence alignment (MSA) and then a state-of-the-art likelihood model is used to reconstruct ancestral indels states. The results are the most probable sequences, together with posterior probabilities for each character and indel at each sequence position for each internal node of the tree. FastML is generic and is applicable for any type of molecular sequences (nucleotide, protein, or codon sequences). drwxr-xr-x root/root 0 2020-12-17 14:31 ./ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/bin/ -rwxr-xr-x root/root 1116416 2020-12-17 14:31 ./usr/bin/fastml -rwxr-xr-x root/root 1771776 2020-12-17 14:31 ./usr/bin/gainLoss -rwxr-xr-x root/root 264448 2020-12-17 14:31 ./usr/bin/indelCoder drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/share/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/share/doc/fastml/ -rw-r--r-- root/root 538 2020-12-17 14:31 ./usr/share/doc/fastml/changelog.Debian.gz -rw-r--r-- root/root 2937 2020-12-17 14:31 ./usr/share/doc/fastml/copyright drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/share/man/ drwxr-xr-x root/root 0 2020-12-17 14:31 ./usr/share/man/man1/ -rw-r--r-- root/root 1491 2020-12-17 14:31 ./usr/share/man/man1/fastml.1.gz -rw-r--r-- root/root 480 2020-12-17 14:31 ./usr/share/man/man1/gainLoss.1.gz -rw-r--r-- root/root 215 2020-12-17 14:31 ./usr/share/man/man1/indelCoder.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [534 B] Get:5 copy:/<>/apt_archive ./ Packages [619 B] Fetched 2116 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-ipv6-perl libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:arm64 t1utils unzip 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 14.0 MB of archives. After this operation, 51.5 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.2 [68.5 kB] Get:4 http://localhost:3142/debian sid/main amd64 openssl amd64 3.0.7-1 [1400 kB] Get:5 http://localhost:3142/debian sid/main amd64 ca-certificates all 20211016 [156 kB] Get:6 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.64-1 [36.6 kB] Get:7 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.5-5 [48.5 kB] Get:8 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.2 [165 kB] Get:9 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1 [564 kB] Get:10 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.40.0-1 [838 kB] Get:11 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1 [948 kB] Get:12 http://localhost:3142/debian sid/main amd64 iso-codes all 4.12.0-1 [2888 kB] Get:13 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:14 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b2 [69.2 kB] Get:15 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:16 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:17 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:18 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:19 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:21 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:23 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.63-1+b1 [44.0 kB] Get:24 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:25 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b1 [123 kB] Get:26 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:27 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:28 http://localhost:3142/debian sid/main amd64 libregexp-ipv6-perl all 0.03-3 [5212 B] Get:29 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.17-1 [90.4 kB] Get:30 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.80-1 [101 kB] Get:31 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.54-1 [224 kB] Get:32 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:33 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.13-2 [19.4 kB] Get:34 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b1 [36.4 kB] Get:35 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1 [13.7 kB] Get:36 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.28-2 [16.4 kB] Get:37 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:38 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.928-3 [9724 B] Get:39 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.112-1 [11.8 kB] Get:40 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.988-1 [51.9 kB] Get:41 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:42 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.32-1+b1 [130 kB] Get:43 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:44 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:45 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:46 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:47 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.58-2 [43.6 kB] Get:48 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b1 [35.2 kB] Get:49 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:50 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:51 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:52 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:53 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b1 [99.5 kB] Get:54 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.30-1 [21.0 kB] Get:55 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:56 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b1 [24.3 kB] Get:57 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b1 [29.4 kB] Get:58 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:59 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:60 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:61 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:62 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.05-2 [10.5 kB] Get:63 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.15-1 [12.6 kB] Get:64 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:65 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:66 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.44-1 [81.7 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.10-1 [24.0 kB] Get:69 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:70 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:71 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.10-1 [19.6 kB] Get:72 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:73 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:74 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.92-2+b1 [317 kB] Get:75 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.078-1 [217 kB] Get:76 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.22-1 [25.3 kB] Get:77 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.10-1 [12.2 kB] Get:78 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:79 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.67-1 [194 kB] Get:80 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:81 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:82 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.023-2 [11.0 kB] Get:83 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.048-3 [33.2 kB] Get:84 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004004-1 [13.3 kB] Get:85 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:86 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.58-3 [36.5 kB] Get:87 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:88 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.13-4 [42.0 kB] Get:89 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:90 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2 [37.0 kB] Get:91 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:92 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:93 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006006-3 [21.0 kB] Get:94 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005004-3 [60.5 kB] Get:95 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:96 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:97 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b3 [170 kB] Get:98 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:99 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3 [10.9 kB] Get:100 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.26-2+b1 [12.6 kB] Get:101 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:102 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.124-1 [56.1 kB] Get:103 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b1 [17.3 kB] Get:104 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1 [11.4 kB] Get:105 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.634-1+b2 [43.1 kB] Get:106 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:107 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.001+ds-1+b1 [102 kB] Get:108 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.001+ds-2 [105 kB] Get:109 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:110 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.30-1 [57.3 kB] Get:111 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.28-1 [28.6 kB] Get:112 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b1 [24.5 kB] Get:113 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b1 [8404 B] Get:114 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.13-2 [12.4 kB] Get:115 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b2 [198 kB] Get:116 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:117 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b1 [73.0 kB] Get:118 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2 [20.2 kB] Get:119 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.15-1 [120 kB] Get:120 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:121 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.84+ds-1+b1 [34.7 kB] Get:122 http://localhost:3142/debian sid/main amd64 plzip amd64 1.10-4 [64.0 kB] Get:123 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:124 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:125 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:126 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-27 [172 kB] Get:127 http://localhost:3142/debian sid/main amd64 lintian all 2.115.3 [1417 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 14.0 MB in 0s (155 MB/s) Selecting previously unselected package netbase. (Reading database ... 21828 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-1.2_all.deb ... Unpacking readline-common (8.2-1.2) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.0.7-1_amd64.deb ... Unpacking openssl (3.0.7-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20211016_all.deb ... Unpacking ca-certificates (20211016) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.64-1_amd64.deb ... Unpacking diffstat (1.64-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../005-libassuan0_2.5.5-5_amd64.deb ... Unpacking libassuan0:amd64 (2.5.5-5) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../006-libreadline8_8.2-1.2_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.2) ... Selecting previously unselected package gpgconf. Preparing to unpack .../007-gpgconf_2.2.40-1_amd64.deb ... Unpacking gpgconf (2.2.40-1) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../008-libsqlite3-0_3.40.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.40.0-1) ... Selecting previously unselected package gpg. Preparing to unpack .../009-gpg_2.2.40-1_amd64.deb ... Unpacking gpg (2.2.40-1) ... Selecting previously unselected package iso-codes. Preparing to unpack .../010-iso-codes_4.12.0-1_all.deb ... Unpacking iso-codes (4.12.0-1) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../011-libaliased-perl_0.34-3_all.deb ... Unpacking libaliased-perl (0.34-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../012-libapt-pkg-perl_0.1.40+b2_amd64.deb ... Unpacking libapt-pkg-perl (0.1.40+b2) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-2+b1_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../014-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../015-libdevel-callchecker-perl_0.008-2_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.008-2) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../016-libparams-classify-perl_0.015-2+b1_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b1) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../017-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../018-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../019-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../020-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../021-libvariable-magic-perl_0.63-1+b1_amd64.deb ... Unpacking libvariable-magic-perl (0.63-1+b1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../022-libb-hooks-endofscope-perl_0.26-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.26-1) ... Selecting previously unselected package libberkeleydb-perl:amd64. Preparing to unpack .../023-libberkeleydb-perl_0.64-2+b1_amd64.deb ... Unpacking libberkeleydb-perl:amd64 (0.64-2+b1) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../024-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../025-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package libregexp-ipv6-perl. Preparing to unpack .../026-libregexp-ipv6-perl_0.03-3_all.deb ... Unpacking libregexp-ipv6-perl (0.03-3) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../027-liburi-perl_5.17-1_all.deb ... Unpacking liburi-perl (5.17-1) ... Selecting previously unselected package libhtml-parser-perl:amd64. 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Unpacking libclone-perl:amd64 (0.46-1) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../034-libconfig-tiny-perl_2.28-2_all.deb ... Unpacking libconfig-tiny-perl (2.28-2) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../035-libparams-util-perl_1.102-2+b1_amd64.deb ... Unpacking libparams-util-perl (1.102-2+b1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../036-libsub-install-perl_0.928-3_all.deb ... Unpacking libsub-install-perl (0.928-3) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../037-libdata-optlist-perl_0.112-1_all.deb ... Unpacking libdata-optlist-perl (0.112-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../038-libsub-exporter-perl_0.988-1_all.deb ... Unpacking libsub-exporter-perl (0.988-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../039-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libcpanel-json-xs-perl:amd64. Preparing to unpack .../040-libcpanel-json-xs-perl_4.32-1+b1_amd64.deb ... Unpacking libcpanel-json-xs-perl:amd64 (4.32-1+b1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../041-libdevel-stacktrace-perl_2.0400-2_all.deb ... Unpacking libdevel-stacktrace-perl (2.0400-2) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../042-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../043-libiterator-perl_0.03+ds1-2_all.deb ... Unpacking libiterator-perl (0.03+ds1-2) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../044-libiterator-util-perl_0.02+ds1-2_all.deb ... Unpacking libiterator-util-perl (0.02+ds1-2) ... Selecting previously unselected package libdata-dpath-perl. Preparing to unpack .../045-libdata-dpath-perl_0.58-2_all.deb ... Unpacking libdata-dpath-perl (0.58-2) ... Selecting previously unselected package libdata-messagepack-perl. Preparing to unpack .../046-libdata-messagepack-perl_1.02-1+b1_amd64.deb ... Unpacking libdata-messagepack-perl (1.02-1+b1) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../047-libnet-domain-tld-perl_1.75-3_all.deb ... Unpacking libnet-domain-tld-perl (1.75-3) ... Selecting previously unselected package libdata-validate-domain-perl. Preparing to unpack .../048-libdata-validate-domain-perl_0.10-1.1_all.deb ... Unpacking libdata-validate-domain-perl (0.10-1.1) ... Selecting previously unselected package libnet-ipv6addr-perl. Preparing to unpack .../049-libnet-ipv6addr-perl_1.02-1_all.deb ... Unpacking libnet-ipv6addr-perl (1.02-1) ... 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Setting up liblz1:amd64 (1.13-4) ... Setting up libberkeleydb-perl:amd64 (0.64-2+b1) ... Setting up plzip (1.10-4) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-2) ... Setting up libmouse-perl (2.5.10-1+b3) ... Setting up libdata-messagepack-perl (1.02-1+b1) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.13-2) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.46-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3) ... Setting up libcpanel-json-xs-perl:amd64 (4.32-1+b1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b1) ... Setting up unzip (6.0-27) ... Setting up libsqlite3-0:amd64 (3.40.0-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.84+ds-1+b1) ... Setting up libio-interactive-perl (1.023-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b1) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:amd64 (2.5.5-5) ... Setting up libconfig-tiny-perl (2.28-2) ... Setting up libsereal-encoder-perl (5.001+ds-2) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.928-3) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004004-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.30-1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.64-1) ... Setting up libvariable-magic-perl (0.63-1+b1) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libregexp-ipv6-perl (0.03-3) ... Setting up libsub-name-perl:amd64 (0.26-2+b1) ... Setting up libsyntax-keyword-try-perl (0.28-1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.634-1+b2) ... Setting up libpath-tiny-perl (0.124-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.048-3) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-3) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libclass-xsaccessor-perl (1.19-4+b1) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b1) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.0.7-1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b1) ... Setting up libperlio-gzip-perl (0.20-1+b1) ... Setting up readline-common (8.2-1.2) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.001+ds-1+b1) ... Setting up libmarkdown2:amd64 (2.2.7-2) ... Setting up liburi-perl (5.17-1) ... Setting up iso-codes (4.12.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.30-1) ... Setting up libemail-address-xs-perl (1.05-1+b1) ... Setting up libnet-ssleay-perl:amd64 (1.92-2+b1) ... Setting up libhttp-date-perl (6.05-2) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.15-1) ... Setting up libreadline8:amd64 (8.2-1.2) ... Setting up libnet-http-perl (6.22-1) ... Setting up libtext-markdown-discount-perl (0.13-2) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 127 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.112-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.80-1) ... Setting up gpgconf (2.2.40-1) ... Setting up libio-socket-ssl-perl (2.078-1) ... Setting up gpg (2.2.40-1) ... Setting up libsub-exporter-perl (0.988-1) ... Setting up libhttp-message-perl (6.44-1) ... Setting up libhtml-form-perl (6.10-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.10-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up libcgi-pm-perl (4.54-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.58-2) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005004-3) ... Setting up liblist-someutils-perl (0.58-3) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.67-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.15-1) ... Setting up liblwp-protocol-https-perl (6.10-1) ... Setting up lintian (2.115.3) ... Setting up sbuild-build-depends-lintian-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.36-6) ... Processing triggers for man-db (2.11.1-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 510832 Build-Time: 318 Distribution: unstable Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 11 Job: fastml_3.11-3 Lintian: pass Machine Architecture: amd64 Package: fastml Package-Time: 338 Source-Version: 3.11-3 Space: 510832 Status: successful Version: 3.11-3 -------------------------------------------------------------------------------- Finished at 2022-12-19T01:56:10Z Build needed 00:05:38, 510832k disk space