sbuild (Debian sbuild) 0.89.3+deb13u4 (28 December 2025) on mjolnir.einval.org +==============================================================================+ | fastml 3.11-5 (amd64) Sun, 22 Mar 2026 02:11:38 +0000 | +==============================================================================+ Package: fastml Version: 3.11-5 Source Version: 3.11-5 Distribution: unstable Machine Architecture: arm64 Host Architecture: amd64 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any I: Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.v4M9KPAV9T... I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Sun, 22 Mar 2026 02:11:54 +0000 | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [187 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [11.5 MB] Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [10.3 MB] Get:4 http://mirror.einval.org/debian unstable/main amd64 Packages [10.4 MB] Fetched 32.3 MB in 7s (4346 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: gcc-16-base libasan8 libatomic1 libcc1-0 libgcc-s1 libgomp1 libhwasan0 libitm1 liblsan0 libssl3t64 libstdc++6 libsystemd0 libtsan2 libubsan1 libudev1 linux-libc-dev openssl-provider-legacy 17 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 15.4 MB of archives. After this operation, 4096 B of additional disk space will be used. Get:1 http://mirror.einval.org/debian unstable/main arm64 libasan8 arm64 16-20260315-1 [2672 kB] Get:2 http://mirror.einval.org/debian unstable/main arm64 libubsan1 arm64 16-20260315-1 [1079 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libtsan2 arm64 16-20260315-1 [2449 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 gcc-16-base arm64 16-20260315-1 [35.4 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libstdc++6 arm64 16-20260315-1 [653 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 liblsan0 arm64 16-20260315-1 [1212 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libitm1 arm64 16-20260315-1 [24.2 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libhwasan0 arm64 16-20260315-1 [1506 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libgomp1 arm64 16-20260315-1 [132 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libcc1-0 arm64 16-20260315-1 [38.8 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libatomic1 arm64 16-20260315-1 [9844 B] Get:12 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1 arm64 16-20260315-1 [53.2 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 openssl-provider-legacy arm64 3.6.1-3 [311 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libssl3t64 arm64 3.6.1-3 [2765 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libsystemd0 arm64 260-1 [405 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libudev1 arm64 260-1 [123 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev all 6.19.8-1 [1949 kB] Fetched 15.4 MB in 0s (90.7 MB/s) (Reading database ... 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Setting up libtsan2:arm64 (16-20260315-1) ... Setting up libcc1-0:arm64 (16-20260315-1) ... Setting up liblsan0:arm64 (16-20260315-1) ... Setting up libitm1:arm64 (16-20260315-1) ... Processing triggers for libc-bin (2.42-13) ... +------------------------------------------------------------------------------+ | Fetch source files Sun, 22 Mar 2026 02:12:16 +0000 | +------------------------------------------------------------------------------+ 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://mirror.einval.org/debian unstable/main fastml 3.11-5 (dsc) [1530 B] Get:2 http://mirror.einval.org/debian unstable/main fastml 3.11-5 (tar) [849 kB] Get:3 http://mirror.einval.org/debian unstable/main fastml 3.11-5 (diff) [10.3 kB] Fetched 861 kB in 0s (11.1 MB/s) Download complete and in download only mode +------------------------------------------------------------------------------+ | Install package build dependencies Sun, 22 Mar 2026 02:12:18 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 Filtered Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:arm64, crossbuild-essential-amd64:arm64, apt-utils:arm64, libc-dev:amd64, libstdc++-dev:amd64 dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/reproducible-path/resolver-IHBd8F/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/reproducible-path/resolver-IHBd8F/apt_archive ./ InRelease Get:2 copy:/build/reproducible-path/resolver-IHBd8F/apt_archive ./ Release [609 B] Ign:3 copy:/build/reproducible-path/resolver-IHBd8F/apt_archive ./ Release.gpg Get:4 copy:/build/reproducible-path/resolver-IHBd8F/apt_archive ./ Sources [715 B] Get:5 copy:/build/reproducible-path/resolver-IHBd8F/apt_archive ./ Packages [758 B] Fetched 2082 B in 0s (95.3 kB/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... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-16-base:amd64 gcc-16-cross-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64 libhwasan0-amd64-cross libitm1:amd64 libitm1-amd64-cross liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libpipeline1 libquadmath0:amd64 libquadmath0-amd64-cross libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring5 libxml2-16 linux-libc-dev-amd64-cross m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-15-locales cpp-15-doc cpp-doc dh-make gcc-15-doc manpages-dev flex bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64 libstdc++-15-doc:amd64 libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:amd64 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu bsdextrautils cpp-15-x86-64-linux-gnu cpp-x86-64-linux-gnu crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-15-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-15-base:amd64 gcc-15-cross-base gcc-15-x86-64-linux-gnu gcc-15-x86-64-linux-gnu-base gcc-16-base:amd64 gcc-16-cross-base gcc-x86-64-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross libatomic1:amd64 libatomic1-amd64-cross libc-gconv-modules-extra:amd64 libc6:amd64 libc6-amd64-cross libc6-dev:amd64 libc6-dev-amd64-cross libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libgcc-15-dev:amd64 libgcc-15-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64 libhwasan0-amd64-cross libitm1:amd64 libitm1-amd64-cross liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc libmagic1t64 libpipeline1 libquadmath0:amd64 libquadmath0-amd64-cross libstdc++-15-dev:amd64 libstdc++-15-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross libtool libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross libuchardet0 libunistring5 libxml2-16 linux-libc-dev-amd64-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:amd64 sensible-utils 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. 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Get:1 copy:/build/reproducible-path/resolver-IHBd8F/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [900 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5+b1 [338 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5+b1 [103 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.46-5+b1 [44.0 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.23.2-1 [242 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2+b1 [69.1 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-10+b1 [1133 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.41.3-4 [98.1 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-2 [40.3 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.1-1+b1 [1455 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.21-1 [323 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.72-6 [494 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.18.1-4 [877 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.23.2-1 [772 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu-base arm64 15.2.0-13cross1 [55.0 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 cpp-15-x86-64-linux-gnu arm64 15.2.0-13cross1 [11.3 MB] Get:19 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:15.2.0-5 [5324 B] Get:20 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.46-3 [1536 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 gcc-15-cross-base all 15.2.0-13cross1 [50.4 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 gcc-16-cross-base all 16-20260315-1cross1 [31.2 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 16-20260315-1cross1 [74.1 kB] Get:24 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 16-20260315-1cross1 [146 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 16-20260315-1cross1 [26.9 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 16-20260315-1cross1 [10.5 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 16-20260315-1cross1 [2879 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 16-20260315-1cross1 [1279 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 16-20260315-1cross1 [2560 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.42-12cross1 [1577 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 16-20260315-1cross1 [743 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 16-20260315-1cross1 [1135 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 16-20260315-1cross1 [1576 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 16-20260315-1cross1 [147 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libgcc-15-dev-amd64-cross all 15.2.0-13cross1 [2706 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 gcc-15-x86-64-linux-gnu arm64 15.2.0-13cross1 [21.8 MB] Get:37 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:15.2.0-5 [1448 B] Get:38 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-amd64-cross all 6.19.8-1 [12.4 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.42-12cross1 [2010 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libstdc++-15-dev-amd64-cross all 15.2.0-13cross1 [2426 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 g++-15-x86-64-linux-gnu arm64 15.2.0-13cross1 [12.2 MB] Get:42 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:15.2.0-5 [1204 B] Get:43 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.12 [3552 B] Get:44 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.31 [75.7 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.5.4-9 [540 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 22 [12.2 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get:50 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.194-4 [182 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.16-3 [99.2 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.4.2-1 [455 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-2+b1 [591 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.23.2-1 [1613 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.22 [216 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.31 [932 kB] Get:58 http://mirror.einval.org/debian unstable/main amd64 gcc-15-base amd64 15.2.0-15 [35.9 kB] Get:59 http://mirror.einval.org/debian unstable/main amd64 gcc-16-base amd64 16-20260315-1 [35.4 kB] Get:60 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 16-20260315-1 [74.1 kB] Get:61 http://mirror.einval.org/debian unstable/main amd64 libc-gconv-modules-extra amd64 2.42-13 [1123 kB] Get:62 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.42-13 [1814 kB] Get:63 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 16-20260315-1 [2888 kB] Get:64 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 16-20260315-1 [10.4 kB] Get:65 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.42-13 [2016 kB] Get:66 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 16-20260315-1 [151 kB] Get:67 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 16-20260315-1 [26.9 kB] Get:68 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 16-20260315-1 [1281 kB] Get:69 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 16-20260315-1 [2572 kB] Get:70 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 16-20260315-1 [765 kB] Get:71 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 16-20260315-1 [1136 kB] Get:72 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 16-20260315-1 [1580 kB] Get:73 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 16-20260315-1 [147 kB] Get:74 http://mirror.einval.org/debian unstable/main amd64 libgcc-15-dev amd64 15.2.0-15 [2719 kB] Get:75 http://mirror.einval.org/debian unstable/main amd64 libstdc++-15-dev amd64 15.2.0-15 [2777 kB] Preconfiguring packages ... Fetched 98.4 MB in 1s (97.0 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 12111 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5+b1_arm64.deb ... Unpacking libmagic-mgc (1:5.46-5+b1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5+b1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-5+b1) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5+b1_arm64.deb ... Unpacking file (1:5.46-5+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.2-1_arm64.deb ... Unpacking gettext-base (0.23.2-1) ... Selecting previously unselected package libuchardet0:arm64. 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Setting up libubsan1-amd64-cross (16-20260315-1cross1) ... Setting up dh-strip-nondeterminism (1.15.0-1) ... Setting up groff-base (1.23.0-10+b1) ... Setting up po-debconf (1.0.22) ... Setting up man-db (2.13.1-1+b1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgcc-15-dev-amd64-cross (15.2.0-13cross1) ... Setting up libstdc++-15-dev-amd64-cross (15.2.0-13cross1) ... Setting up debhelper (13.31) ... Setting up gcc-15-x86-64-linux-gnu (15.2.0-13cross1) ... Setting up g++-15-x86-64-linux-gnu (15.2.0-13cross1) ... Setting up gcc-x86-64-linux-gnu (4:15.2.0-5) ... Setting up g++-x86-64-linux-gnu (4:15.2.0-5) ... Setting up crossbuild-essential-amd64 (12.12) ... Setting up libgcc-s1:amd64 (16-20260315-1) ... Setting up libc6:amd64 (2.42-13) ... Setting up libhwasan0:amd64 (16-20260315-1) ... Setting up libasan8:amd64 (16-20260315-1) ... Setting up libc6-dev:amd64 (2.42-13) ... Setting up libtsan2:amd64 (16-20260315-1) ... Setting up libstdc++6:amd64 (16-20260315-1) ... Setting up liblsan0:amd64 (16-20260315-1) ... Setting up libitm1:amd64 (16-20260315-1) ... Setting up libgomp1:amd64 (16-20260315-1) ... Setting up libquadmath0:amd64 (16-20260315-1) ... Setting up libatomic1:amd64 (16-20260315-1) ... Setting up libubsan1:amd64 (16-20260315-1) ... Setting up libgcc-15-dev:amd64 (15.2.0-15) ... Setting up libstdc++-15-dev:amd64 (15.2.0-15) ... Setting up sbuild-build-depends-main-dummy:amd64 (0.invalid.0) ... Processing triggers for base-files (14) ... Processing triggers for libc-bin (2.42-13) ... +------------------------------------------------------------------------------+ | Check architectures Sun, 22 Mar 2026 02:13:08 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Sun, 22 Mar 2026 02:13:09 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.57+deb13-arm64 #1 SMP Debian 6.12.57-1 (2025-11-05) arm64 (aarch64) Toolchain package versions: binutils_2.46-3 dpkg-dev_1.23.7 g++-15_15.2.0-15 gcc-15_15.2.0-15 libc6-dev_2.42-13 libstdc++-15-dev_15.2.0-15 libstdc++-15-dev-amd64-cross_15.2.0-13cross1 libstdc++6_16-20260315-1 libstdc++6-amd64-cross_16-20260315-1cross1 linux-libc-dev_6.19.8-1 Package versions: apt_3.1.16 apt-utils_3.1.16 autoconf_2.72-6 automake_1:1.18.1-4 autopoint_0.23.2-1 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8+b1 bash_5.3-2 binutils_2.46-3 binutils-aarch64-linux-gnu_2.46-3 binutils-common_2.46-3 binutils-x86-64-linux-gnu_2.46-3 bsdextrautils_2.41.3-4 build-essential_12.12 bzip2_1.0.8-6+b1 coreutils_9.10-1 cpp_4:15.2.0-5 cpp-15_15.2.0-15 cpp-15-aarch64-linux-gnu_15.2.0-15 cpp-15-x86-64-linux-gnu_15.2.0-13cross1 cpp-aarch64-linux-gnu_4:15.2.0-5 cpp-x86-64-linux-gnu_4:15.2.0-5 crossbuild-essential-amd64_12.12 dash_0.5.12-12+b1 debconf_1.5.92 debhelper_13.31 debian-archive-keyring_2025.1 debianutils_5.23.2+b1 dh-autoreconf_22 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1+b1 dpkg_1.23.7 dpkg-dev_1.23.7 dwz_0.16-3 file_1:5.46-5+b1 findutils_4.10.0-3+b1 g++_4:15.2.0-5 g++-15_15.2.0-15 g++-15-aarch64-linux-gnu_15.2.0-15 g++-15-x86-64-linux-gnu_15.2.0-13cross1 g++-aarch64-linux-gnu_4:15.2.0-5 g++-x86-64-linux-gnu_4:15.2.0-5 gcc_4:15.2.0-5 gcc-15_15.2.0-15 gcc-15-aarch64-linux-gnu_15.2.0-15 gcc-15-base_15.2.0-15 gcc-15-cross-base_15.2.0-13cross1 gcc-15-x86-64-linux-gnu_15.2.0-13cross1 gcc-15-x86-64-linux-gnu-base_15.2.0-13cross1 gcc-16-base_16-20260315-1 gcc-16-cross-base_16-20260315-1cross1 gcc-aarch64-linux-gnu_4:15.2.0-5 gcc-x86-64-linux-gnu_4:15.2.0-5 gettext_0.23.2-1 gettext-base_0.23.2-1 grep_3.12-1+b1 groff-base_1.23.0-10+b1 gzip_1.13-1+b1 hostname_3.25+b1 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-3 libapt-pkg7.0_3.1.16 libarchive-zip-perl_1.68-1 libasan8_16-20260315-1 libasan8-amd64-cross_16-20260315-1cross1 libatomic1_16-20260315-1 libatomic1-amd64-cross_16-20260315-1cross1 libattr1_1:2.5.2-4 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1+b1 libbinutils_2.46-3 libblkid1_2.41.3-4 libbz2-1.0_1.0.8-6+b1 libc-bin_2.42-13 libc-dev-bin_2.42-13 libc-gconv-modules-extra_2.42-13 libc6_2.42-13 libc6-amd64-cross_2.42-12cross1 libc6-dev_2.42-13 libc6-dev-amd64-cross_2.42-12cross1 libcap-ng0_0.9.1-1 libcc1-0_16-20260315-1 libcrypt1_1:4.5.1-1 libctf-nobfd0_2.46-3 libctf0_2.46-3 libdb5.3t64_5.3.28+dfsg2-11 libdebconfclient0_0.282+b2 libdebhelper-perl_13.31 libdpkg-perl_1.23.7 libelf1t64_0.194-4 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-15 libgcc-15-dev-amd64-cross_15.2.0-13cross1 libgcc-s1_16-20260315-1 libgcc-s1-amd64-cross_16-20260315-1cross1 libgdbm-compat4t64_1.26-1+b1 libgdbm6t64_1.26-1+b1 libgmp10_2:6.3.0+dfsg-5+b1 libgomp1_16-20260315-1 libgomp1-amd64-cross_16-20260315-1cross1 libgprofng0_2.46-3 libhogweed6t64_3.10.2-1 libhwasan0_16-20260315-1 libhwasan0-amd64-cross_16-20260315-1cross1 libisl23_0.27-1+b1 libitm1_16-20260315-1 libitm1-amd64-cross_16-20260315-1cross1 libjansson4_2.14-2+b4 liblsan0_16-20260315-1 liblsan0-amd64-cross_16-20260315-1cross1 liblz4-1_1.10.0-8 liblzma5_5.8.2-2 libmagic-mgc_1:5.46-5+b1 libmagic1t64_1:5.46-5+b1 libmd0_1.1.0-2+b2 libmount1_2.41.3-4 libmpc3_1.3.1-2+b1 libmpfr6_4.2.2-2+b1 libnettle8t64_3.10.2-1 libpam-modules_1.7.0-5+b1 libpam-modules-bin_1.7.0-5+b1 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5+b1 libpcre2-8-0_10.46-1+b1 libperl5.40_5.40.1-7 libpipeline1_1.5.8-2 libquadmath0_16-20260315-1 libquadmath0-amd64-cross_16-20260315-1cross1 libseccomp2_2.6.0-2+b1 libselinux1_3.9-4+b1 libsframe3_2.46-3 libsmartcols1_2.41.3-4 libssl3t64_3.6.1-3 libstdc++-15-dev_15.2.0-15 libstdc++-15-dev-amd64-cross_15.2.0-13cross1 libstdc++6_16-20260315-1 libstdc++6-amd64-cross_16-20260315-1cross1 libsystemd0_260-1 libtinfo6_6.6+20251231-1 libtool_2.5.4-9 libtsan2_16-20260315-1 libtsan2-amd64-cross_16-20260315-1cross1 libubsan1_16-20260315-1 libubsan1-amd64-cross_16-20260315-1cross1 libuchardet0_0.0.8-2+b1 libudev1_260-1 libunistring5_1.4.2-1 libuuid1_2.41.3-4 libxml2-16_2.15.1+dfsg-2+b1 libxxhash0_0.8.3-2+b1 libzstd1_1.5.7+dfsg-3+b1 linux-libc-dev_6.19.8-1 linux-libc-dev-amd64-cross_6.19.8-1 login_1:4.16.0-2+really2.41.3-4 login.defs_1:4.19.3-1 m4_1.4.21-1 make_4.4.1-3+b1 man-db_2.13.1-1+b1 mawk_1.3.4.20260302-1 ncurses-base_6.6+20251231-1 ncurses-bin_6.6+20251231-1 openssl-provider-legacy_3.6.1-3 patch_2.8-2+b1 perl_5.40.1-7 perl-base_5.40.1-7 perl-modules-5.40_5.40.1-7 po-debconf_1.0.22 rpcsvc-proto_1.4.3-1+b2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2+b2 sensible-utils_0.0.26 sqv_1.3.0-5 sysvinit-utils_3.15-6+b1 tar_1.35+dfsg-4 util-linux_2.41.3-4 xz-utils_5.8.2-2 zlib1g_1:1.3.dfsg+really1.3.1-3 +------------------------------------------------------------------------------+ | Build Sun, 22 Mar 2026 02:13:09 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: fastml Binary: fastml Architecture: any Version: 3.11-5 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fastml.tau.ac.il/ Standards-Version: 4.7.3 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 2d3b0a60bf69e58e394db1363cb833ea337365eb 10332 fastml_3.11-5.debian.tar.xz Checksums-Sha256: 2d1ec87116eae1163177631ad39083db01cdd78ffb8d119bebbdbb6a43e99451 849058 fastml_3.11.orig.tar.gz 4d85694516ae1911ac0f16d83537d0d243a6d22580096f2949cd705a107d0e4e 10332 fastml_3.11-5.debian.tar.xz Files: 4443e346151ff347816dcba7e700212d 849058 fastml_3.11.orig.tar.gz e0143f9c9dd0b5fa6137bf0e7cfb3a76 10332 fastml_3.11-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmmm2dcACgkQQc5/C58b izIrTQf+MJk2Geh4TsBrNdDmM9TPhvfDxmlfdY9yGs9dJ3SGCvhx+StUUmqs4DRH ztXczOg+AomrUFE8v847fv/aQMVCoT1i08BMUV0zGrtTq2QcuTBrvFdClZP+VeD5 K5P/IQ2wyPp5DphPLIBtF8+zWE8gaZ9NOytEJx2u+PUwjUDnylT+0Rp3ng0diSkB clN+SsP6qvJorxvYeCP/6TBEDFC15LU3BQ7zC7x5d4s5sbd62ObKRc9qJh5pw73t syWKqmp0tNFc2PK2g+heXrokumiYE1Bic/I1yQO4L/JmWY5e+U7HYqA7qyaIOPnJ nzKDy0eSvIoPHuwHiRBUkMond+K35w== =OSLZ -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./fastml_3.11-5.dsc: missing OpenPGP keyrings dpkg-source: info: verifying ./fastml_3.11-5.dsc dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-keyring.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-tag2upload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-nonupload.pgp dpkg-source: info: skipping absent keyring /usr/share/keyrings/debian-maintainers.pgp dpkg-source: info: extracting fastml in /build/reproducible-path/fastml-3.11 dpkg-source: info: unpacking fastml_3.11.orig.tar.gz dpkg-source: info: unpacking fastml_3.11-5.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.amd64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=sbuild PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SHELL=/bin/sh USER=sbuild dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B --jobs-try=1 dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Santiago Vila dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/fastml-3.11' dh_auto_clean make -j1 clean make[2]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make clean make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs' cd phylogeny && make clean make[4]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' cd programs;make clean make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make clean make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' cd gainLoss && make clean make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' cd indelCoder && make clean make[4]: Entering directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/indelCoder' make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep rm -rf bin find libs/phylogeny/tests -type f -executable -delete make[1]: Leaving directory '/build/reproducible-path/fastml-3.11' 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=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc make[1]: Entering directory '/build/reproducible-path/fastml-3.11' cd libs;make all make[2]: Entering directory '/build/reproducible-path/fastml-3.11/libs' cd phylogeny && make all make[3]: Entering directory '/build/reproducible-path/fastml-3.11/libs/phylogeny' making depend x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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; | ^~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 | ^~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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): | ^~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp In file included from /usr/x86_64-linux-gnu/include/c++/15/ostream:42, from /usr/x86_64-linux-gnu/include/c++/15/iostream:43, 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:76:3: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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:76:3: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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:76:3, inlined from ‘virtual void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble&, int)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:39:108: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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; | ^~~~ 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/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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; | ^~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp In member function ‘virtual void generalGammaDistribution::setGammaParameters(int, double, double)’, inlined from ‘generalGammaDistribution::generalGammaDistribution(double, double, int)’ at generalGammaDistribution.cpp:34:20: generalGammaDistribution.cpp:56:26: warning: ‘*this.generalGammaDistribution::_alpha’ is used uninitialized [-Wuninitialized] 56 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) | ^~~~~~ generalGammaDistribution.cpp:56:49: warning: ‘*this.generalGammaDistribution::_beta’ may be used uninitialized [-Wmaybe-uninitialized] 56 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) | ^~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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): | ^~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp In file included from generalGammaDistributionPlusInvariant.h:9, from simulateWithDependence.h:35, from simulateWithDependence.cpp:1: distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 269 | dist = myNRmethod(ax,bx,cx, | ~~~~~~~~~~^~~~~~~~~~ 270 | C_evalLikeDist_d(ctc,_sp), | ~~~~~~~~~~~~~~~~~~~~~~~~~~ 271 | C_evalLikeDist_d2(ctc,_sp), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 272 | tol, | ~~~~ 273 | 100, | ~~~~ 274 | zeroFound);// max it for NR; | ~~~~~~~~~~ likeDist.cpp:210:13: warning: variable ‘oldIntervalSize’ set but not used [-Wunused-but-set-variable] 210 | MDOUBLE oldIntervalSize = currentIntervalSize; | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp likelihoodComputation.cpp: In function ‘double likelihoodComputation::getTreeLikelihoodAllPosAlphTheSame(const tree&, const sequenceContainer&, const stochasticProcess&, const Vdouble*, unObservableData*)’: likelihoodComputation.cpp:43:45: warning: ‘LforMissingData’ may be used uninitialized [-Wmaybe-uninitialized] 43 | LofPos = LofPos / (1- LforMissingData); | ~~^~~~~~~~~~~~~~~~~~ likelihoodComputation.cpp:27:17: note: ‘LforMissingData’ was declared here 27 | MDOUBLE LforMissingData; | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp In file included from /usr/x86_64-linux-gnu/include/c++/15/cassert:46, 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 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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;isize() == 4) && (other._alphabet->size()%4 == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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(); | ^~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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(); | ^~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp In file included from distanceBasedSeqs2Tree.cpp:3: distanceBasedSeqs2Tree.h:50:16: warning: ‘virtual tree iterativeDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble*, const tree*)’ was hidden [-Woverloaded-virtual=] 50 | virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:105:18: note: by ‘tree commonAlphaDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, double, const Vdouble*, const tree*)’ 105 | tree seqs2TreeBootstrap(const sequenceContainer &sc, const MDOUBLE alpha, const Vdouble *weights, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:50:16: warning: ‘virtual tree iterativeDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble*, const tree*)’ was hidden [-Woverloaded-virtual=] 50 | virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:137:18: note: by ‘tree rate4siteDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble&, const Vdouble*, const tree*)’ 137 | tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble &rates, const Vdouble *weights, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:50:16: warning: ‘virtual tree iterativeDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble*, const tree*)’ was hidden [-Woverloaded-virtual=] 50 | virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:173:18: note: by ‘tree posteriorDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const VVdoubleRep&, const Vdouble*, const tree*)’ 173 | tree seqs2TreeBootstrap(const sequenceContainer &sc, const VVdoubleRep &posterior, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ 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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp In file included from pairwiseGammaDistance.h:6, from pairwiseGammaDistance.cpp:3: likeDist.h:51:19: warning: ‘virtual const double likeDist::giveDistance(const sequence&, const sequence&, const std::vector*, double*) const’ was hidden [-Woverloaded-virtual=] 51 | const MDOUBLE giveDistance(const sequence& s1, | ^~~~~~~~~~~~ pairwiseGammaDistance.h:32:19: note: by ‘const double pairwiseGammaDistance::giveDistance(const sequence&, const sequence&, const std::vector*, double*, double*) const’ 32 | const MDOUBLE giveDistance(const sequence& s1, | ^~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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) : | ^~~~~~~~~~~~~~~~ In member function ‘virtual void betaDistribution::setBetaParameters(int, double, double)’, inlined from ‘betaDistribution::betaDistribution(double, double, int, discretizationType)’ at betaDistribution.cpp:36:19: betaDistribution.cpp:72:26: warning: ‘*this.betaDistribution::_alpha’ is used uninitialized [-Wuninitialized] 72 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) | ^~~~~~ betaDistribution.cpp:72:49: warning: ‘*this.betaDistribution::_beta’ may be used uninitialized [-Wmaybe-uninitialized] 72 | if ((in_alpha == _alpha) && (in_beta == _beta) && (in_number_of_categories == categories())) | ^~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp In file included from ssrvDistanceSeqs2Tree.h:6, from ssrvDistanceSeqs2Tree.cpp:3: distanceBasedSeqs2Tree.h:50:16: warning: ‘virtual tree iterativeDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble*, const tree*)’ was hidden [-Woverloaded-virtual=] 50 | virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:105:18: note: by ‘tree commonAlphaDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, double, const Vdouble*, const tree*)’ 105 | tree seqs2TreeBootstrap(const sequenceContainer &sc, const MDOUBLE alpha, const Vdouble *weights, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:50:16: warning: ‘virtual tree iterativeDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble*, const tree*)’ was hidden [-Woverloaded-virtual=] 50 | virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:137:18: note: by ‘tree rate4siteDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble&, const Vdouble*, const tree*)’ 137 | tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble &rates, const Vdouble *weights, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:50:16: warning: ‘virtual tree iterativeDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble*, const tree*)’ was hidden [-Woverloaded-virtual=] 50 | virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:173:18: note: by ‘tree posteriorDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const VVdoubleRep&, const Vdouble*, const tree*)’ 173 | tree seqs2TreeBootstrap(const sequenceContainer &sc, const VVdoubleRep &posterior, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ distanceBasedSeqs2Tree.h:50:16: warning: ‘virtual tree iterativeDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, const Vdouble*, const tree*)’ was hidden [-Woverloaded-virtual=] 50 | virtual tree seqs2TreeBootstrap(const sequenceContainer &sc, const Vdouble *weights=NULL, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ ssrvDistanceSeqs2Tree.h:41:18: note: by ‘tree ssrvDistanceSeqs2Tree::seqs2TreeBootstrap(const sequenceContainer&, double, double, const Vdouble*, const tree*)’ 41 | tree seqs2TreeBootstrap(const sequenceContainer &sc, const MDOUBLE alpha, MDOUBLE nu, const Vdouble *weights, const tree* constraintTreePtr=NULL); | ^~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp In file included from generalGammaDistributionPlusInvariant.h:9, from generalGammaDistributionPlusInvariant.cpp:1: distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp In file included from gammaDistributionPlusInvariant.h:9, from gammaDistributionPlusInvariant.cpp:1: distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ gammaDistributionPlusInvariant.h:19:7: note: by ‘gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)’ 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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) | ^~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 seqeuncesFilter.h:6, from seqeuncesFilter.cpp:1: In member function ‘const sequence& sequenceContainer::operator[](int) const’, inlined from ‘static void seqeuncesFilter::removeSequencesWithInserts(sequenceContainer&, const sequenceContainer&, int, const std::string&, std::string)’ at seqeuncesFilter.cpp:175:16: sequenceContainer.h:31:88: warning: ‘refID’ may be used uninitialized [-Wmaybe-uninitialized] 31 | const sequence& operator[](const int id) const {return _seqDataVec[_id2place[id]];} | ^ 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; | ^~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp mixtureDistribution.cpp: In member function ‘virtual const double mixtureDistribution::rates(int) const’: mixtureDistribution.cpp:221:40: warning: ‘componentNum’ may be used uninitialized [-Wmaybe-uninitialized] 221 | return _components[componentNum]->rates(categoryInComponent) * _globalRate; | ^ mixtureDistribution.cpp:210:13: note: ‘componentNum’ was declared here 210 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~ mixtureDistribution.cpp:221:48: warning: ‘categoryInComponent’ may be used uninitialized [-Wmaybe-uninitialized] 221 | return _components[componentNum]->rates(categoryInComponent) * _globalRate; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:210:27: note: ‘categoryInComponent’ was declared here 210 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ In file included from mixtureDistribution.cpp:1: In member function ‘const double mixtureDistribution::getComponentProb(int) const’, inlined from ‘virtual const double mixtureDistribution::ratesProb(int) const’ at mixtureDistribution.cpp:239:26: mixtureDistribution.h:40:102: warning: ‘componentNum’ may be used uninitialized [-Wmaybe-uninitialized] 40 | const MDOUBLE getComponentProb(int componentNum) const {return _componentsWeight[componentNum] / _totalWeight;} | ^ 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; | ^~~~~~~~~~~~ mixtureDistribution.cpp:239:86: warning: ‘categoryInComponent’ may be used uninitialized [-Wmaybe-uninitialized] 239 | return getComponentProb(componentNum) * _components[componentNum]->ratesProb(categoryInComponent); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:228:27: note: ‘categoryInComponent’ was declared here 228 | int componentNum, categoryInComponent, totalCat = 0; | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/15/x86_64-linux-gnu/bits/c++allocator.h:33, from /usr/x86_64-linux-gnu/include/c++/15/bits/allocator.h:46, from /usr/x86_64-linux-gnu/include/c++/15/vector:65, from definitions.h:18, from mixtureDistribution.h:11: In member function ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]’, inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]’ at /usr/x86_64-linux-gnu/include/c++/15/bits/alloc_traits.h:674:17, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]’ at /usr/x86_64-linux-gnu/include/c++/15/bits/stl_vector.h:1421:30, inlined from ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’ at mixtureDistribution.cpp:52:24: /usr/x86_64-linux-gnu/include/c++/15/bits/new_allocator.h:191:11: warning: ‘pComp’ may be used uninitialized [-Wmaybe-uninitialized] 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’: mixtureDistribution.cpp:40:43: note: ‘pComp’ declared here 40 | generalGammaDistribution* pComp; | ^~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/15/vector:68: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]’, inlined from ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’ at mixtureDistribution.cpp:52:24: /usr/x86_64-linux-gnu/include/c++/15/bits/stl_vector.h:1427:28: warning: ‘pComp’ may be used uninitialized [-Wmaybe-uninitialized] 1427 | _M_realloc_append(__x); | ~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/15/vector:74: /usr/x86_64-linux-gnu/include/c++/15/bits/vector.tcc: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’: /usr/x86_64-linux-gnu/include/c++/15/bits/vector.tcc:557:7: note: by argument 2 of type ‘generalGammaDistribution* const&’ to ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*; _Alloc = std::allocator]’ declared here 557 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:40:43: note: ‘pComp’ declared here 40 | generalGammaDistribution* pComp; | ^~~~~ In member function ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]’, inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]’ at /usr/x86_64-linux-gnu/include/c++/15/bits/alloc_traits.h:674:17, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]’ at /usr/x86_64-linux-gnu/include/c++/15/bits/stl_vector.h:1421:30, inlined from ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’ at mixtureDistribution.cpp:84:24: /usr/x86_64-linux-gnu/include/c++/15/bits/new_allocator.h:191:11: warning: ‘pComp’ may be used uninitialized [-Wmaybe-uninitialized] 191 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); } | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’: mixtureDistribution.cpp:72:43: note: ‘pComp’ declared here 72 | generalGammaDistribution* pComp; | ^~~~~ In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]’, inlined from ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’ at mixtureDistribution.cpp:84:24: /usr/x86_64-linux-gnu/include/c++/15/bits/stl_vector.h:1427:28: warning: ‘pComp’ may be used uninitialized [-Wmaybe-uninitialized] 1427 | _M_realloc_append(__x); | ~~~~~~~~~~~~~~~~~^~~~~ /usr/x86_64-linux-gnu/include/c++/15/bits/vector.tcc: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’: /usr/x86_64-linux-gnu/include/c++/15/bits/vector.tcc:557:7: note: by argument 2 of type ‘generalGammaDistribution* const&’ to ‘void std::vector<_Tp, _Alloc>::_M_realloc_append(_Args&& ...) [with _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*; _Alloc = std::allocator]’ declared here 557 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:72:43: note: ‘pComp’ declared here 72 | generalGammaDistribution* pComp; | ^~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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; | ^~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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))); | ^~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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))); | ^~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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; | ^~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp In file included from simulateRateShiftJumps.h:4, from simulateRateShiftJumps.cpp:1: simulateJumpsAbstract.h:30:22: warning: ‘virtual void simulateJumpsAbstract::runSimulation(int)’ was hidden [-Woverloaded-virtual=] 30 | virtual void runSimulation(int iterNum = 10000); | ^~~~~~~~~~~~~ simulateRateShiftJumps.h:16:14: note: by ‘void simulateRateShiftJumps::runSimulation(int, std::vector)’ 16 | void runSimulation(int iterNum, vector inputNodes); | ^~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 '/build/reproducible-path/fastml-3.11/libs/phylogeny' make[2]: Leaving directory '/build/reproducible-path/fastml-3.11/libs' cd programs;make all make[2]: Entering directory '/build/reproducible-path/fastml-3.11/programs' cd fastml && make all make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/fastml' making depend x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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() { | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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() { | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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() { | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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() { | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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() { | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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() { | ^~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 ) : | ^~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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; | ^~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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; | ^~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -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 x86_64-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml make[3]: Leaving directory '/build/reproducible-path/fastml-3.11/programs/fastml' cd gainLoss && make all make[3]: Entering directory '/build/reproducible-path/fastml-3.11/programs/gainLoss' making depend x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp 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::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::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; | ^~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp In file included from gainLoss.h:30, from gainLoss.cpp:20: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../../libs/phylogeny/distributionPlusInvariant.h: At global scope: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLoss.cpp:25: ../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by ‘gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)’ 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLoss.cpp:41: 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 member function ‘void gainLossModelNonReversible::updateQ()’, inlined from ‘void gainLossModelNonReversible::setMu2(double)’ at gainLossModel.h:156:10, inlined from ‘void gainLoss::initParamsAtRandPoints(int, stochasticProcess*, unObservableData*, std::ostream&)’ at gainLoss.cpp:1857:100: gainLossModel.h:173:28: warning: ‘currM2’ may be used uninitialized [-Wmaybe-uninitialized] 173 | _Q[1][1] = -_loss; | ^~~~~~ 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; | ^~~~~~ gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector >&, distribution*, distribution*, unObservableData*, std::ostream&)’: gainLoss.cpp:1974:39: warning: ‘currGainBeta’ may be used uninitialized [-Wmaybe-uninitialized] 1974 | updateGainBeta(currGainBeta,spVVec,gainDist,lossDist); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:1940:17: note: ‘currGainBeta’ was declared here 1940 | MDOUBLE currGainBeta; | ^~~~~~~~~~~~ gainLoss.cpp:1978:40: warning: ‘currLossAlpha’ may be used uninitialized [-Wmaybe-uninitialized] 1978 | updateLossAlpha(currLossAlpha,spVVec,gainDist,lossDist); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:1942:17: note: ‘currLossAlpha’ was declared here 1942 | MDOUBLE currLossAlpha; // Loss (for non-reversible model only) | ^~~~~~~~~~~~~ gainLoss.cpp:1980:47: warning: ‘currLossBeta’ may be used uninitialized [-Wmaybe-uninitialized] 1980 | updateLossBeta(currLossBeta,spVVec,gainDist,lossDist); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:1943:17: note: ‘currLossBeta’ was declared here 1943 | MDOUBLE currLossBeta; | ^~~~~~~~~~~~ gainLoss.cpp:1982:56: warning: ‘currLossProbInvariant’ may be used uninitialized [-Wmaybe-uninitialized] 1982 | updateLossProbInvariant(currLossProbInvariant,lossDist); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:1944:17: note: ‘currLossProbInvariant’ was declared here 1944 | MDOUBLE currLossProbInvariant; | ^~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:2031:50: warning: ‘bestGainProbInvariant’ may be used uninitialized [-Wmaybe-uninitialized] 2031 | if(probInvariant) updateGainProbInvariant(bestGainProbInvariant,gainDist); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss.cpp:1930:17: note: ‘bestGainProbInvariant’ was declared here 1930 | MDOUBLE bestGainProbInvariant = 0.5; | ^~~~~~~~~~~~~~~~~~~~~ In file included from /usr/x86_64-linux-gnu/include/c++/15/ostream:42, from /usr/x86_64-linux-gnu/include/c++/15/iostream:43, 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::printLikelihoodLandscape(stochasticProcess*)’ at gainLoss.cpp:3896:33: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘AlphaRate’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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; | ^~~~~~~~~ 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:3896:62: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘Loss’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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:3896:74: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘Theta’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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; | ^~~~~ gainLoss.cpp: In member function ‘void gainLoss::printLikelihoodLandscapeStatFreqRatioAndRootFreqRatio()’: 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: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: In member function ‘void gainLoss::startStochasticProcess()’: gainLoss.cpp:865:83: warning: ‘rateDist’ may be used uninitialized [-Wmaybe-uninitialized] 865 | _sp = new stochasticProcess(rateDist,pijAcc,gainLossOptions::_isReversible); | ^ gainLoss.cpp:806:23: note: ‘rateDist’ was declared here 806 | distribution* rateDist; | ^~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::startStochasticProcessVec()’: gainLoss.cpp:1124:117: warning: ‘rateDist’ may be used uninitialized [-Wmaybe-uninitialized] 1124 | stochasticProcess* sp = new stochasticProcess(rateDist,pijAcc,gainLossOptions::_isReversible); | ^ gainLoss.cpp:1105:39: note: ‘rateDist’ was declared here 1105 | distribution* rateDist; | ^~~~~~~~ gainLoss.cpp: In member function ‘void gainLoss::computeCoEvolutionScoresBasedOnSimulatedData(sequenceContainer&)’: gainLoss.cpp:2484:22: warning: ‘countsGL’ may be used uninitialized [-Wmaybe-uninitialized] 2484 | countsGL->run(); | ~~~~~~~~~~~~~^~ 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; | ^~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossUtils.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gainLossUtils.cpp:19: gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ ../../libs/phylogeny/distributionPlusInvariant.h: At global scope: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.cpp:20: ../../libs/phylogeny/gammaDistributionPlusInvariant.h:19:7: note: by ‘gammaDistributionPlusInvariant& gammaDistributionPlusInvariant::operator=(const gammaDistributionPlusInvariant&)’ 19 | class gammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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; | ^~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, from optimizeGainLossModel.h:27, from optimizeGainLossModel.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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; | ^~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, from optimizeGainLossModelVV.h:27, from optimizeGainLossModelVV.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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; | ^~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, from gainLossModel.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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): | ^~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from siteSpecificGL.cpp:23: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from siteSpecificGL.cpp:24: gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from gainLossModel.h:27, from computePosteriorExpectationOfChange.cpp:25: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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/x86_64-linux-gnu/include/c++/15/ostream:42, from /usr/x86_64-linux-gnu/include/c++/15/iostream:43, 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:230:3: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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; | ^~~~ 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:230:3: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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:230:3: /usr/x86_64-linux-gnu/include/c++/15/bits/ostream.h:232:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 232 | { 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; | ^~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from gainLoss.h:30, from gainLossProject.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from gainLoss.h:30, from gainLossOptimizer.h:24, from gainLossOptimizer.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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; | ^~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp In file included from gainLoss.h:30, from rate4siteGL.h:24, from rate4siteGL.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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; | ^~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp In file included from gainLoss.h:30, from computeCountsGL.h:24, from computeCountsGL.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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): | ^~~~~~~~~~~~~~~ x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/build/reproducible-path/fastml-3.11=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp In file included from gainLoss.h:30, from computeCorrelations.h:25, from computeCorrelations.cpp:17: ../../libs/phylogeny/distributionPlusInvariant.h:17:44: warning: ‘virtual distributionPlusInvariant& distributionPlusInvariant::operator=(const distributionPlusInvariant&)’ was hidden [-Woverloaded-virtual=] 17 | virtual distributionPlusInvariant& operator=(const distributionPlusInvariant& other); | ^~~~~~~~ In file included from gainLossUtils.h:27, from gainLossModel.h:27, from gainLoss.h:35: ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:19:7: note: by ‘generalGammaDistributionPlusInvariant& generalGammaDistributionPlusInvariant::operator=(const generalGammaDistributionPlusInvariant&)’ 19 | class generalGammaDistributionPlusInvariant : public distributionPlusInvariant { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:58:32: warning: ‘virtual gainLossModel& gainLossModel::operator=(const gainLossModel&)’ was hidden [-Woverloaded-virtual=] 58 | virtual gainLossModel& operator=(const gainLossModel &other); | ^~~~~~~~ gainLossModel.h:124:7: note: by ‘gainLossModelNonReversible& gainLossModelNonReversible::operator=(const gainLossModelNonReversible&)’ 124 | class gainLossModelNonReversible : public gainLossModel { | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLossModel.h:95:25: warning: ‘virtual double gainLossModel::updateQ(bool)’ was hidden [-Woverloaded-virtual=] 95 | virtual MDOUBLE updateQ(bool isReversible); | ^~~~~~~ gainLossModel.h:171:14: note: by ‘void gainLossModelNonReversible::updateQ()’ 171 | void updateQ(){ | ^~~~~~~ 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