sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | fastml 3.11-4 (ppc64el) Sun, 28 Jan 2024 19:05:54 +0000 | +==============================================================================+ Package: fastml Version: 3.11-4 Source Version: 3.11-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: ppc64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-3910af6e-c7ef-4e6b-a17f-24e92054396f' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-j0tYs5/resolver-VJpKGy' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [198 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2024-01-28-1407.32-F-2024-01-28-0206.35.pdiff [18.4 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2024-01-28-1407.32-F-2024-01-28-0206.35.pdiff [86.8 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2024-01-28-1407.32-F-2024-01-28-0206.35.pdiff [18.4 kB] Get:6 http://localhost:3142/debian sid/main ppc64el Packages [9515 kB] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2024-01-28-1407.32-F-2024-01-28-0206.35.pdiff [86.8 kB] Fetched 9945 kB in 3s (3523 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'fastml' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/fastml.git Please use: git clone https://salsa.debian.org/med-team/fastml.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 861 kB of source archives. Get:1 http://localhost:3142/debian sid/main fastml 3.11-4 (dsc) [1900 B] Get:2 http://localhost:3142/debian sid/main fastml 3.11-4 (tar) [849 kB] Get:3 http://localhost:3142/debian sid/main fastml 3.11-4 (diff) [10.2 kB] Fetched 861 kB in 0s (69.7 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/fastml-j0tYs5/fastml-3.11' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-j0tYs5' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64, libc-dev:ppc64el, libstdc++-dev:ppc64el Filtered Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64, libc-dev:ppc64el, libstdc++-dev:ppc64el dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [720 B] Get:5 copy:/<>/apt_archive ./ Packages [765 B] Fetched 2094 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-powerpc64le-linux-gnu bsdextrautils cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-11-base:ppc64el gcc-13-cross-base gcc-13-powerpc64le-linux-gnu gcc-13-powerpc64le-linux-gnu-base gcc-14-base:ppc64el gcc-14-cross-base gcc-powerpc64le-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:ppc64el libasan8-ppc64el-cross libatomic1:ppc64el libatomic1-ppc64el-cross libc6:ppc64el libc6-dev:ppc64el libc6-dev-ppc64el-cross libc6-ppc64el-cross libcom-err2:ppc64el libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:ppc64el libcrypt1:ppc64el libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:ppc64el libgcc-13-dev-ppc64el-cross libgcc-s1:ppc64el libgcc-s1-ppc64el-cross libgomp1:ppc64el libgomp1-ppc64el-cross libgssapi-krb5-2:ppc64el libicu72 libio-string-perl libitm1:ppc64el libitm1-ppc64el-cross libk5crypto3:ppc64el libkeyutils1:ppc64el libkrb5-3:ppc64el libkrb5support0:ppc64el liblocale-gettext-perl liblsan0:ppc64el liblsan0-ppc64el-cross libmagic-mgc libmagic1 libnsl-dev:ppc64el libnsl2:ppc64el libpipeline1 libquadmath0:ppc64el libquadmath0-ppc64el-cross libssl3:ppc64el libstdc++-11-dev:ppc64el libstdc++-13-dev-ppc64el-cross libstdc++6:ppc64el libstdc++6-ppc64el-cross libsub-override-perl libtirpc-dev:ppc64el libtirpc3:ppc64el libtool libtsan0:ppc64el libtsan2-ppc64el-cross libubsan1:ppc64el libubsan1-ppc64el-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-ppc64el-cross m4 man-db po-debconf sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-13-locales cpp-13-doc cpp-doc dh-make binutils-multiarch gcc-13-doc manpages-dev flex bison gdb-powerpc64le-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:ppc64el libc-l10n:ppc64el locales:ppc64el libnss-nis:ppc64el libnss-nisplus:ppc64el manpages-dev:ppc64el krb5-doc:ppc64el krb5-user:ppc64el libstdc++-11-doc:ppc64el libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libidn2-0:ppc64el libarchive-cpio-perl krb5-locales:ppc64el libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-powerpc64le-linux-gnu bsdextrautils cpp-13-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-13-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-11-base:ppc64el gcc-13-cross-base gcc-13-powerpc64le-linux-gnu gcc-13-powerpc64le-linux-gnu-base gcc-14-base:ppc64el gcc-14-cross-base gcc-powerpc64le-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan6:ppc64el libasan8-ppc64el-cross libatomic1:ppc64el libatomic1-ppc64el-cross libc6:ppc64el libc6-dev:ppc64el libc6-dev-ppc64el-cross libc6-ppc64el-cross libcom-err2:ppc64el libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:ppc64el libcrypt1:ppc64el libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:ppc64el libgcc-13-dev-ppc64el-cross libgcc-s1:ppc64el libgcc-s1-ppc64el-cross libgomp1:ppc64el libgomp1-ppc64el-cross libgssapi-krb5-2:ppc64el libicu72 libio-string-perl libitm1:ppc64el libitm1-ppc64el-cross libk5crypto3:ppc64el libkeyutils1:ppc64el libkrb5-3:ppc64el libkrb5support0:ppc64el liblocale-gettext-perl liblsan0:ppc64el liblsan0-ppc64el-cross libmagic-mgc libmagic1 libnsl-dev:ppc64el libnsl2:ppc64el libpipeline1 libquadmath0:ppc64el libquadmath0-ppc64el-cross libssl3:ppc64el libstdc++-11-dev:ppc64el libstdc++-13-dev-ppc64el-cross libstdc++6:ppc64el libstdc++6-ppc64el-cross libsub-override-perl libtirpc-dev:ppc64el libtirpc3:ppc64el libtool libtsan0:ppc64el libtsan2-ppc64el-cross libubsan1:ppc64el libubsan1-ppc64el-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-ppc64el-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:ppc64el sensible-utils ucf 0 upgraded, 102 newly installed, 0 to remove and 0 not upgraded. Need to get 95.7 MB of archives. After this operation, 401 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [920 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-6+b1 [15.2 kB] Get:3 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:4 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-2+b1 [314 kB] Get:5 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.45-2+b1 [105 kB] Get:6 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-2+b1 [43.1 kB] Get:7 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-14 [161 kB] Get:8 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.8-1 [68.5 kB] Get:9 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-3 [1180 kB] Get:10 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.39.3-6 [89.4 kB] Get:11 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1+b2 [38.1 kB] Get:12 http://localhost:3142/debian sid/main amd64 man-db amd64 2.12.0-3 [1401 kB] Get:13 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:14 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB] Get:15 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:16 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:17 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:18 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-14 [496 kB] Get:19 http://localhost:3142/debian sid/main amd64 binutils-powerpc64le-linux-gnu amd64 2.41.90.20240122-1 [2765 kB] Get:20 http://localhost:3142/debian sid/main amd64 gcc-13-powerpc64le-linux-gnu-base amd64 13.2.0-12cross1 [42.7 kB] Get:21 http://localhost:3142/debian sid/main amd64 cpp-13-powerpc64le-linux-gnu amd64 13.2.0-12cross1 [9190 kB] Get:22 http://localhost:3142/debian sid/main amd64 cpp-powerpc64le-linux-gnu amd64 4:13.2.0-4 [4680 B] Get:23 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:24 http://localhost:3142/debian sid/main amd64 gcc-13-cross-base all 13.2.0-12cross1 [38.1 kB] Get:25 http://localhost:3142/debian sid/main amd64 gcc-14-cross-base all 14-20240127-1cross1 [37.9 kB] Get:26 http://localhost:3142/debian sid/main amd64 libc6-ppc64el-cross all 2.37-12cross1 [1352 kB] Get:27 http://localhost:3142/debian sid/main amd64 libgcc-s1-ppc64el-cross all 14-20240127-1cross1 [35.5 kB] Get:28 http://localhost:3142/debian sid/main amd64 libgomp1-ppc64el-cross all 14-20240127-1cross1 [134 kB] Get:29 http://localhost:3142/debian sid/main amd64 libitm1-ppc64el-cross all 14-20240127-1cross1 [27.9 kB] Get:30 http://localhost:3142/debian sid/main amd64 libatomic1-ppc64el-cross all 14-20240127-1cross1 [9544 B] Get:31 http://localhost:3142/debian sid/main amd64 libasan8-ppc64el-cross all 14-20240127-1cross1 [2641 kB] Get:32 http://localhost:3142/debian sid/main amd64 liblsan0-ppc64el-cross all 14-20240127-1cross1 [1201 kB] Get:33 http://localhost:3142/debian sid/main amd64 libtsan2-ppc64el-cross all 14-20240127-1cross1 [2408 kB] Get:34 http://localhost:3142/debian sid/main amd64 libstdc++6-ppc64el-cross all 14-20240127-1cross1 [749 kB] Get:35 http://localhost:3142/debian sid/main amd64 libubsan1-ppc64el-cross all 14-20240127-1cross1 [1078 kB] Get:36 http://localhost:3142/debian sid/main amd64 libquadmath0-ppc64el-cross all 14-20240127-1cross1 [151 kB] Get:37 http://localhost:3142/debian sid/main amd64 libgcc-13-dev-ppc64el-cross all 13.2.0-12cross1 [1370 kB] Get:38 http://localhost:3142/debian sid/main amd64 gcc-13-powerpc64le-linux-gnu amd64 13.2.0-12cross1 [17.6 MB] Get:39 http://localhost:3142/debian sid/main amd64 gcc-powerpc64le-linux-gnu amd64 4:13.2.0-4 [1460 B] Get:40 http://localhost:3142/debian sid/main amd64 linux-libc-dev-ppc64el-cross all 6.5.8-1cross1 [2004 kB] Get:41 http://localhost:3142/debian sid/main amd64 libc6-dev-ppc64el-cross all 2.37-12cross1 [1811 kB] Get:42 http://localhost:3142/debian sid/main amd64 libstdc++-13-dev-ppc64el-cross all 13.2.0-12cross1 [2296 kB] Get:43 http://localhost:3142/debian sid/main amd64 g++-13-powerpc64le-linux-gnu amd64 13.2.0-12cross1 [10.1 MB] Get:44 http://localhost:3142/debian sid/main amd64 g++-powerpc64le-linux-gnu amd64 4:13.2.0-4 [1208 B] Get:45 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:46 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:47 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:48 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:49 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:50 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:51 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:52 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b2 [313 kB] Get:53 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:54 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.31-1 [64.8 kB] Get:55 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:56 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:57 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:58 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:59 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:60 http://localhost:3142/debian sid/main amd64 crossbuild-essential-ppc64el all 12.10 [3492 B] Get:61 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.13 [85.0 kB] Get:62 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB] Get:63 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:64 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:65 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.10-1 [10.6 kB] Get:66 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:67 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:68 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.190-1+b1 [176 kB] Get:69 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:70 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-14 [1300 kB] Get:71 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:72 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:73 http://localhost:3142/debian sid/main amd64 debhelper all 13.13 [889 kB] Get:74 http://localhost:3142/debian sid/main ppc64el gcc-11-base ppc64el 11.4.0-7 [40.3 kB] Get:75 http://localhost:3142/debian sid/main ppc64el gcc-14-base ppc64el 14-20240127-1 [42.1 kB] Get:76 http://localhost:3142/debian sid/main ppc64el libgcc-s1 ppc64el 14-20240127-1 [35.5 kB] Get:77 http://localhost:3142/debian sid/main ppc64el libc6 ppc64el 2.37-14 [2679 kB] Get:78 http://localhost:3142/debian sid/main ppc64el libasan6 ppc64el 11.4.0-7 [2037 kB] Get:79 http://localhost:3142/debian sid/main ppc64el libatomic1 ppc64el 14-20240127-1 [9864 B] Get:80 http://localhost:3142/debian sid/main ppc64el libcrypt1 ppc64el 1:4.4.36-4 [98.1 kB] Get:81 http://localhost:3142/debian sid/main ppc64el libcrypt-dev ppc64el 1:4.4.36-4 [132 kB] Get:82 http://localhost:3142/debian sid/main ppc64el libkrb5support0 ppc64el 1.20.1-5 [36.2 kB] Get:83 http://localhost:3142/debian sid/main ppc64el libcom-err2 ppc64el 1.47.0-2+b1 [20.5 kB] Get:84 http://localhost:3142/debian sid/main ppc64el libk5crypto3 ppc64el 1.20.1-5 [89.8 kB] Get:85 http://localhost:3142/debian sid/main ppc64el libkeyutils1 ppc64el 1.6.3-2+b2 [10.4 kB] Get:86 http://localhost:3142/debian sid/main ppc64el libssl3 ppc64el 3.1.4-2 [2043 kB] Get:87 http://localhost:3142/debian sid/main ppc64el libkrb5-3 ppc64el 1.20.1-5 [364 kB] Get:88 http://localhost:3142/debian sid/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-5 [149 kB] Get:89 http://localhost:3142/debian sid/main ppc64el libtirpc3 ppc64el 1.3.4+ds-1 [93.3 kB] Get:90 http://localhost:3142/debian sid/main ppc64el libnsl2 ppc64el 1.3.0-3 [44.3 kB] Get:91 http://localhost:3142/debian sid/main ppc64el libtirpc-dev ppc64el 1.3.4+ds-1 [206 kB] Get:92 http://localhost:3142/debian sid/main ppc64el libnsl-dev ppc64el 1.3.0-3 [72.7 kB] Get:93 http://localhost:3142/debian sid/main ppc64el libc6-dev ppc64el 2.37-14 [1817 kB] Get:94 http://localhost:3142/debian sid/main ppc64el libgomp1 ppc64el 14-20240127-1 [142 kB] Get:95 http://localhost:3142/debian sid/main ppc64el libitm1 ppc64el 14-20240127-1 [28.5 kB] Get:96 http://localhost:3142/debian sid/main ppc64el liblsan0 ppc64el 14-20240127-1 [1201 kB] Get:97 http://localhost:3142/debian sid/main ppc64el libtsan0 ppc64el 11.4.0-7 [2022 kB] Get:98 http://localhost:3142/debian sid/main ppc64el libstdc++6 ppc64el 14-20240127-1 [799 kB] Get:99 http://localhost:3142/debian sid/main ppc64el libubsan1 ppc64el 14-20240127-1 [1079 kB] Get:100 http://localhost:3142/debian sid/main ppc64el libquadmath0 ppc64el 14-20240127-1 [151 kB] Get:101 http://localhost:3142/debian sid/main ppc64el libgcc-11-dev ppc64el 11.4.0-7 [1273 kB] Get:102 http://localhost:3142/debian sid/main ppc64el libstdc++-11-dev ppc64el 11.4.0-7 [2072 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 95.7 MB in 0s (192 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 16272 files and directories currently installed.) Preparing to unpack .../000-liblocale-gettext-perl_1.07-6+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-6+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../001-sensible-utils_0.0.20_all.deb ... Unpacking sensible-utils (0.0.20) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../002-libmagic-mgc_1%3a5.45-2+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-2+b1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../003-libmagic1_1%3a5.45-2+b1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.45-2+b1) ... Selecting previously unselected package file. Preparing to unpack .../004-file_1%3a5.45-2+b1_amd64.deb ... Unpacking file (1:5.45-2+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../005-gettext-base_0.21-14_amd64.deb ... Unpacking gettext-base (0.21-14) ... 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Setting up sensible-utils (0.0.20) ... Setting up libuchardet0:amd64 (0.0.8-1) ... Setting up linux-libc-dev-ppc64el-cross (6.5.8-1cross1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libgcc-s1-ppc64el-cross (14-20240127-1cross1) ... Setting up binutils-powerpc64le-linux-gnu (2.41.90.20240122-1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up cpp-13-powerpc64le-linux-gnu (13.2.0-12cross1) ... Setting up libelf1:amd64 (0.190-1+b1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up liblocale-gettext-perl (1.07-6+b1) ... Setting up cpp-powerpc64le-linux-gnu (4:13.2.0-4) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-14) ... Setting up libc6-dev-ppc64el-cross (2.37-12cross1) ... Setting up libtool (2.4.7-7) ... Setting up libquadmath0-ppc64el-cross (14-20240127-1cross1) ... Setting up libasan8-ppc64el-cross (14-20240127-1cross1) ... Setting up liblsan0-ppc64el-cross (14-20240127-1cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libtsan2-ppc64el-cross (14-20240127-1cross1) ... Setting up dh-autoreconf (20) ... Setting up ucf (3.0043+nmu1) ... Setting up libstdc++6-ppc64el-cross (14-20240127-1cross1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.23.0-3) ... Setting up libubsan1-ppc64el-cross (14-20240127-1cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-3) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libgcc-13-dev-ppc64el-cross (13.2.0-12cross1) ... Setting up libstdc++-13-dev-ppc64el-cross (13.2.0-12cross1) ... Setting up debhelper (13.13) ... Setting up gcc-13-powerpc64le-linux-gnu (13.2.0-12cross1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up g++-13-powerpc64le-linux-gnu (13.2.0-12cross1) ... Setting up gcc-powerpc64le-linux-gnu (4:13.2.0-4) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up g++-powerpc64le-linux-gnu (4:13.2.0-4) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-ppc64el (12.10) ... Setting up libgcc-s1:ppc64el (14-20240127-1) ... Setting up libc6:ppc64el (2.37-14) ... Setting up libstdc++6:ppc64el (14-20240127-1) ... Setting up liblsan0:ppc64el (14-20240127-1) ... Setting up libitm1:ppc64el (14-20240127-1) ... Setting up libtsan0:ppc64el (11.4.0-7) ... Setting up libkeyutils1:ppc64el (1.6.3-2+b2) ... Setting up libssl3:ppc64el (3.1.4-2) ... Setting up libcrypt1:ppc64el (1:4.4.36-4) ... Setting up libcom-err2:ppc64el (1.47.0-2+b1) ... Setting up libgomp1:ppc64el (14-20240127-1) ... Setting up libasan6:ppc64el (11.4.0-7) ... Setting up libkrb5support0:ppc64el (1.20.1-5) ... Setting up libquadmath0:ppc64el (14-20240127-1) ... Setting up libatomic1:ppc64el (14-20240127-1) ... Setting up libk5crypto3:ppc64el (1.20.1-5) ... Setting up libubsan1:ppc64el (14-20240127-1) ... Setting up libgcc-11-dev:ppc64el (11.4.0-7) ... Setting up libcrypt-dev:ppc64el (1:4.4.36-4) ... Setting up libkrb5-3:ppc64el (1.20.1-5) ... Setting up libgssapi-krb5-2:ppc64el (1.20.1-5) ... Setting up libtirpc3:ppc64el (1.3.4+ds-1) ... Setting up libtirpc-dev:ppc64el (1.3.4+ds-1) ... Setting up libnsl2:ppc64el (1.3.0-3) ... Setting up libnsl-dev:ppc64el (1.3.0-3) ... Setting up libc6-dev:ppc64el (2.37-14) ... Setting up libstdc++-11-dev:ppc64el (11.4.0-7) ... Setting up sbuild-build-depends-main-dummy:ppc64el (0.invalid.0) ... Processing triggers for libc-bin (2.37-14) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.55-1 (2023-09-29) amd64 (x86_64) Toolchain package versions: binutils_2.41.90.20240122-1 dpkg-dev_1.22.4 g++-11_11.4.0-7 g++-13_13.2.0-12 gcc-11_11.4.0-7 gcc-13_13.2.0-12 libc6-dev_2.37-14 libstdc++-11-dev_11.4.0-7 libstdc++-13-dev_13.2.0-12 libstdc++-13-dev-ppc64el-cross_13.2.0-12cross1 libstdc++6_14-20240127-1 libstdc++6-ppc64el-cross_14-20240127-1cross1 linux-libc-dev_6.6.13-1 Package versions: adduser_3.137 apt_2.7.10 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41.90.20240122-1 binutils-common_2.41.90.20240122-1 binutils-powerpc64le-linux-gnu_2.41.90.20240122-1 binutils-x86-64-linux-gnu_2.41.90.20240122-1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.4-3+b1 cpp_4:13.2.0-4 cpp-11_11.4.0-7 cpp-13_13.2.0-12 cpp-13-powerpc64le-linux-gnu_13.2.0-12cross1 cpp-13-x86-64-linux-gnu_13.2.0-12 cpp-powerpc64le-linux-gnu_4:13.2.0-4 cpp-x86-64-linux-gnu_4:13.2.0-4 cross-config_2.6.20 crossbuild-essential-ppc64el_12.10 dash_0.5.12-6 debconf_1.5.85 debhelper_13.13 debian-archive-keyring_2023.4 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.4 dpkg-cross_2.6.20 dpkg-dev_1.22.4 dwz_0.15-1 e2fsprogs_1.47.0-2+b1 fakeroot_1.33-1 file_1:5.45-2+b1 findutils_4.9.0-5 g++_4:13.2.0-4 g++-11_11.4.0-7 g++-13_13.2.0-12 g++-13-powerpc64le-linux-gnu_13.2.0-12cross1 g++-13-x86-64-linux-gnu_13.2.0-12 g++-powerpc64le-linux-gnu_4:13.2.0-4 g++-x86-64-linux-gnu_4:13.2.0-4 gcc_4:13.2.0-4 gcc-11_11.4.0-7 gcc-11-base_11.4.0-7 gcc-12-base_12.3.0-14 gcc-13_13.2.0-12 gcc-13-base_13.2.0-12 gcc-13-cross-base_13.2.0-12cross1 gcc-13-powerpc64le-linux-gnu_13.2.0-12cross1 gcc-13-powerpc64le-linux-gnu-base_13.2.0-12cross1 gcc-13-x86-64-linux-gnu_13.2.0-12 gcc-14-base_14-20240127-1 gcc-14-cross-base_14-20240127-1cross1 gcc-9-base_9.5.0-4 gcc-powerpc64le-linux-gnu_4:13.2.0-4 gcc-x86-64-linux-gnu_4:13.2.0-4 gettext_0.21-14 gettext-base_0.21-14 gpgv_2.2.40-1.1+b1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-1 libapt-pkg6.0_2.7.10 libarchive-zip-perl_1.68-1 libasan6_11.4.0-7 libasan8_14-20240127-1 libasan8-ppc64el-cross_14-20240127-1cross1 libatomic1_14-20240127-1 libatomic1-ppc64el-cross_14-20240127-1cross1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2 libaudit1_1:3.1.2-2 libbinutils_2.41.90.20240122-1 libblkid1_2.39.3-6 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-14 libc-dev-bin_2.37-14 libc6_2.37-14 libc6-dev_2.37-14 libc6-dev-ppc64el-cross_2.37-12cross1 libc6-ppc64el-cross_2.37-12cross1 libcap-ng0_0.8.4-1 libcap2_1:2.66-4+b2 libcc1-0_14-20240127-1 libcom-err2_1.47.0-2+b1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.41.90.20240122-1 libctf0_2.41.90.20240122-1 libdb5.3_5.3.28+dfsg2-4+b1 libdebconfclient0_0.271 libdebhelper-perl_13.13 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.22.4 libelf1_0.190-1+b1 libext2fs2_1.47.0-2+b1 libfakeroot_1.33-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-11-dev_11.4.0-7 libgcc-13-dev_13.2.0-12 libgcc-13-dev-ppc64el-cross_13.2.0-12cross1 libgcc-s1_14-20240127-1 libgcc-s1-ppc64el-cross_14-20240127-1cross1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.3-1 libgomp1_14-20240127-1 libgomp1-ppc64el-cross_14-20240127-1cross1 libgpg-error0_1.47-3 libgprofng0_2.41.90.20240122-1 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhwasan0_14-20240127-1 libicu72_72.1-4 libidn2-0_2.3.7-1 libio-string-perl_1.08-4 libisl23_0.26-3+b2 libitm1_14-20240127-1 libitm1-ppc64el-cross_14-20240127-1cross1 libjansson4_2.14-2+b2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2+b2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 liblocale-gettext-perl_1.07-6+b1 liblsan0_14-20240127-1 liblsan0-ppc64el-cross_14-20240127-1cross1 liblz4-1_1.9.4-1+b2 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2+b1 libmagic1_1:5.45-2+b1 libmd0_1.1.0-2 libmount1_2.39.3-6 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1 libnettle8_3.9.1-2 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-4 libpam-modules_1.5.2-9.1+b1 libpam-modules-bin_1.5.2-9.1+b1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1+b1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.34_5.34.0-5 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1+b2 libquadmath0_14-20240127-1 libquadmath0-ppc64el-cross_14-20240127-1cross1 libseccomp2_2.5.5-1 libselinux1_3.5-2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b2 libsepol2_3.5-2 libsframe1_2.41.90.20240122-1 libsmartcols1_2.39.3-6 libss2_1.47.0-2+b1 libssl3_3.1.4-2 libstdc++-11-dev_11.4.0-7 libstdc++-13-dev_13.2.0-12 libstdc++-13-dev-ppc64el-cross_13.2.0-12cross1 libstdc++6_14-20240127-1 libstdc++6-ppc64el-cross_14-20240127-1cross1 libsub-override-perl_0.10-1 libsystemd0_255.3-1 libtasn1-6_4.19.0-3+b2 libtext-glob-perl_0.11-3 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libtsan0_11.4.0-7 libtsan2_14-20240127-1 libtsan2-ppc64el-cross_14-20240127-1cross1 libubsan1_14-20240127-1 libubsan1-ppc64el-cross_14-20240127-1cross1 libuchardet0_0.0.8-1 libudev1_255.3-1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-6 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b2 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.3+b2 libxxhash0_0.8.2-2 libyaml-perl_1.31-1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.6.13-1 linux-libc-dev-ppc64el-cross_6.5.8-1cross1 login_1:4.13+dfsg1-3+b1 logsave_1.47.0-2+b1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 mount_2.39.3-6 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 passwd_1:4.13+dfsg1-3+b1 patch_2.7.6-7 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.34_5.34.0-5 perl-modules-5.38_5.38.2-3 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.20 sysvinit-utils_3.08-6 tar_1.35+dfsg-3 tzdata_2023d-1 ucf_3.0043+nmu1 usrmerge_39 util-linux_2.39.3-6 util-linux-extra_2.39.3-6 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: fastml Binary: fastml Architecture: any Version: 3.11-4 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: http://fastml.tau.ac.il/ Standards-Version: 4.6.2 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 7530d47e861350740cb869801c1ac13b844ada7f 10164 fastml_3.11-4.debian.tar.xz Checksums-Sha256: 2d1ec87116eae1163177631ad39083db01cdd78ffb8d119bebbdbb6a43e99451 849058 fastml_3.11.orig.tar.gz 31206f832cf5500066e5e5dfd448b224c2a410bf265e3961ea2ddb84a37fc191 10164 fastml_3.11-4.debian.tar.xz Files: 4443e346151ff347816dcba7e700212d 849058 fastml_3.11.orig.tar.gz c2d36bf402afb8462c79bfbead23547e 10164 fastml_3.11-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWxO1cRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFxTQ/+P6vte5yk0+ZDdWEcoa3cZlVp57GH26N1 siM2zI/ZaDPJRP9wOxtbpBPv335pctuRbeWDO1j6iVVd/RuK0nz4Cnys5yQVX4bw 8f6lpXQ85DncnepGSG8o5849lFSDP0/oP0pJAL23RzIcFFKICYnGRBSdbvuFlcKh lk1hfntISLhQJy/Mb/Yxr5avQxTqrR5V34yDn9e2jb7ozp5C4Iov5Opwac1ZdAdW lURcm+5VqEDnrCF5mqpJMSgS9ikIPBhLQqFVDt3UkiEZyJk5VQ8PWr3LRw/HVC0z 3nEyEG1rLSw1hLJeN96qLfl2R9VGsT4Eg9J+7xBvzuK6YeDNRahgKmE4GGBrGShI dIhJdkTtssLsI7TX++Y4uNynMR1BDYHzgl0EkPMxoZA7JGUsyyX/lNXu96F9eqpY IqlUL04fuoj+7laVetWzZ8HIFPU7TYxMffiJORAv+0o/CI6DKzgDykByoNX+1LCP M/b4cEE2M1NxjweShL1zw25u451LsJZiFSWjYYJpqVb0M+7MXb6Lhv8DmK5dVD1m AbymUv1TkUumxNjrAOo5KVOC7ToPmHN+aPtTeCaBVIR4PpHvxFbe5QCsTROGIQGX 0eU8q+oZ4wwmWz5evixLgXUHqh8IuQsRRzGBA0/iVNBSN8ziB8ntImLkc4lWRN10 f+RrC7uPnwU= =SAiw -----END PGP SIGNATURE----- gpgv: Signature made Wed Jan 24 16:31:19 2024 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./fastml_3.11-4.dsc: no acceptable signature found dpkg-source: info: extracting fastml in /<> dpkg-source: info: unpacking fastml_3.11.orig.tar.gz dpkg-source: info: unpacking fastml_3.11-4.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.ppc64el DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.OXs4vsSsYK/sbuild.conf SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-3910af6e-c7ef-4e6b-a17f-24e92054396f SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -appc64el -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package fastml dpkg-buildpackage: info: source version 3.11-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type powerpc64le-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture ppc64el debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>' dh_auto_clean make -j1 clean make[2]: Entering directory '/<>' cd libs;make clean make[3]: Entering directory '/<>/libs' cd phylogeny && make clean make[4]: Entering directory '/<>/libs/phylogeny' rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a *.o make[4]: Leaving directory '/<>/libs/phylogeny' make[3]: Leaving directory '/<>/libs' cd programs;make clean make[3]: Entering directory '/<>/programs' cd fastml && make clean make[4]: Entering directory '/<>/programs/fastml' rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml fastml.debug fastml.doubleRep *.o make[4]: Leaving directory '/<>/programs/fastml' cd gainLoss && make clean make[4]: Entering directory '/<>/programs/gainLoss' rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss gainLoss.debug gainLoss.doubleRep *.o make[4]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make clean make[4]: Entering directory '/<>/programs/indelCoder' rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder indelCoder.debug indelCoder.doubleRep *.o make[4]: Leaving directory '/<>/programs/indelCoder' make[3]: Leaving directory '/<>/programs' make[2]: Leaving directory '/<>' rm -f libs/phylogeny/make.dep \ programs/fastml/make.dep \ programs/gainLoss/make.dep \ programs/indelCoder/make.dep rm -rf bin find libs/phylogeny/tests -type f -executable -delete make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a dh_auto_build -a make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-gcc make[1]: Entering directory '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/libs/phylogeny' making depend powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o AddLog.o AddLog.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiProp.o NNiProp.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o NNiSep.o NNiSep.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Nni.o Nni.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o aaJC.o aaJC.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTrees.o allTrees.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o alphabet.o alphabet.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o amino.o amino.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlpha.o bestAlpha.cpp bestAlpha.cpp: In constructor ‘bestAlphaAndBetaAndBBL::bestAlphaAndBetaAndBBL(tree&, const sequenceContainer&, stochasticProcess&, const Vdouble*, double, double, double, double, double, double, double, int, int)’: bestAlpha.cpp:371:17: warning: variable ‘oldA’ set but not used [-Wunused-but-set-variable] 371 | MDOUBLE oldA=0; | ^~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp bestAlphaManyTrees.cpp: In function ‘void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector&, std::vector&, const std::vector*>*, std::vector&, double&, int, double)’: bestAlphaManyTrees.cpp:184:17: warning: variable ‘ax’ set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ bestAlphaManyTrees.cpp:184:20: warning: variable ‘bx’ set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ bestAlphaManyTrees.cpp:184:23: warning: variable ‘cx’ set but not used [-Wunused-but-set-variable] 184 | MDOUBLE ax,bx,cx; // left, midle, right limit on alpha | ^~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestHKYparam.o bestHKYparam.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bootstrap.o bootstrap.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM.o bblEM.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMfixRoot.o bblEMfixRoot.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProprtional.o bblEMProprtional.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEMSeperate.o bblEMSeperate.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o clustalFormat.o clustalFormat.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codon.o codon.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonJC.o codonJC.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeCounts.o computeCounts.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeDownAlg.o computeDownAlg.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeMarginalAlg.o computeMarginalAlg.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePijComponent.o computePijComponent.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlg.o computeUpAlg.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp In file included from computeSubstitutionCounts.cpp:1: computeSubstitutionCounts.h: In constructor ‘computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer&, const tree&, multipleStochasticProcess*, std::string&, VVVdouble&, int, double, bool)’: computeSubstitutionCounts.h:57:19: warning: ‘computeSubstitutionCounts::_LpostPerSpPerCat’ will be initialized after [-Wreorder] 57 | VVVdouble _LpostPerSpPerCat; // _LpostPerSpPerCat[sp][rateCat][pos] | ^~~~~~~~~~~~~~~~~ computeSubstitutionCounts.h:53:13: warning: ‘int computeSubstitutionCounts::_simulationsIterNum’ [-Wreorder] 53 | int _simulationsIterNum; | ^~~~~~~~~~~~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): | ^~~~~~~~~~~~~~~~~~~~~~~~~ computeSubstitutionCounts.h:54:17: warning: ‘computeSubstitutionCounts::_probCutOffSum’ will be initialized after [-Wreorder] 54 | MDOUBLE _probCutOffSum; | ^~~~~~~~~~~~~~ computeSubstitutionCounts.h:52:14: warning: ‘bool computeSubstitutionCounts::_isSilent’ [-Wreorder] 52 | bool _isSilent; | ^~~~~~~~~ computeSubstitutionCounts.cpp:15:1: warning: when initialized here [-Wreorder] 15 | computeSubstitutionCounts::computeSubstitutionCounts(const sequenceContainer& sc, const tree& tr, multipleStochasticProcess* MultSpPtr, string& outDir, VVVdouble& LpostPerSpPerCat, const int simulationsIterNum, const MDOUBLE probCutOffSum, bool isSilent): | ^~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp In file included from /usr/powerpc64le-linux-gnu/include/c++/13/iostream:41, 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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; | ^~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ConversionUtils.o ConversionUtils.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o countTableComponent.o countTableComponent.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o datMatrixHolder.o datMatrixHolder.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceTable.o distanceTable.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distribution.o distribution.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o errorMsg.o errorMsg.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastStartTree.o fastStartTree.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fastaFormat.o fastaFormat.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o findRateOfGene.o findRateOfGene.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp In file included from fromCountTableComponentToDistancePropEB.cpp:3: fromCountTableComponentToDistancePropEB.h: In constructor ‘fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector >&, int, multipleStochasticProcess*, const gammaDistribution*, double, double)’: fromCountTableComponentToDistancePropEB.h:29:19: warning: ‘fromCountTableComponentToDistancePropEB::_nodeID’ will be initialized after [-Wreorder] 29 | const int _nodeID; | ^~~~~~~ fromCountTableComponentToDistancePropEB.h:28:34: warning: ‘const gammaDistribution* fromCountTableComponentToDistancePropEB::_pProportionDist’ [-Wreorder] 28 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ fromCountTableComponentToDistancePropEB.cpp:6:1: warning: when initialized here [-Wreorder] 6 | fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromQtoPt.o fromQtoPt.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistribution.o gammaDistribution.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaUtilities.o gammaUtilities.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistribution.o generalGammaDistribution.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o getRandomWeights.o getRandomWeights.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o goldmanYangModel.o goldmanYangModel.cpp goldmanYangModel.cpp: In constructor ‘goldmanYangModel::goldmanYangModel(double, double, codon&, bool)’: goldmanYangModel.cpp:8:1: warning: ‘goldmanYangModel::_globalV’ is initialized with itself [-Winit-self] 8 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK,codon & inCodonAlph, const bool globalV): | ^~~~~~~~~~~~~~~~ goldmanYangModel.cpp: In constructor ‘goldmanYangModel::goldmanYangModel(double, double, codon&, const Vdouble&, bool)’: goldmanYangModel.cpp:18:1: warning: ‘goldmanYangModel::_globalV’ is initialized with itself [-Winit-self] 18 | goldmanYangModel::goldmanYangModel(const MDOUBLE inV, const MDOUBLE inK, codon & inCodonAlph,const Vdouble& freq,const bool globalV): | ^~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o hky.o hky.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateWithDependence.o simulateWithDependence.cpp 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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o KH_calculation.o KH_calculation.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist.o likeDist.cpp likeDist.cpp: In instantiation of ‘double myNRmethod(double, double, double, regF, dF, double, int, int&) [with regF = C_evalLikeDist_d; dF = C_evalLikeDist_d2]’: likeDist.cpp:269:22: required from here likeDist.cpp:210:13: warning: variable ‘oldIntervalSize’ set but not used [-Wunused-but-set-variable] 210 | MDOUBLE oldIntervalSize = currentIntervalSize; | ^~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistfixRoot.o likeDistfixRoot.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistProp.o likeDistProp.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDistPropEB.o likeDistPropEB.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation.o likelihoodComputation.cpp 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; | ^~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logFile.o logFile.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o maseFormat.o maseFormat.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o molphyFormat.o molphyFormat.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nexusFormat.o nexusFormat.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nj.o nj.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o njConstrain.o njConstrain.cpp In file included from /usr/powerpc64le-linux-gnu/include/c++/13/cassert:44, from njConstrain.cpp:4: njConstrain.cpp: In function ‘tree::TreeNode* joinNodesToSubtree(tree&, tree::TreeNode*&, tree::TreeNode*&)’: njConstrain.cpp:92:12: warning: suggest parentheses around assignment used as truth value [-Wparentheses] 92 | assert (k=fatherNode->getNumberOfSons()+2); // both s1 and s2 should have been skiped | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucJC.o nucJC.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o nucleotide.o nucleotide.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o numRec.o numRec.cpp numRec.cpp:306:2: warning: "/*" within comment [-Wcomment] 306 | //* for (i=1;i>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o Parameters.o Parameters.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipFormat.o phylipFormat.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pijAccelerator.o pijAccelerator.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readDatMatrix.o readDatMatrix.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o readTree.o readTree.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o recognizeFormat.o recognizeFormat.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModel.o replacementModel.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o searchStatus.o searchStatus.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequence.o sequence.cpp sequence.cpp: In constructor ‘sequence::sequence(const sequence&, const alphabet*)’: sequence.cpp:76:42: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses] 76 | || (inAlph->size() == 4) && (other._alphabet->size()%4 == 0)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o sequenceContainer.o sequenceContainer.cpp sequenceContainer.cpp: In member function ‘void sequenceContainer::removeGapPositions()’: sequenceContainer.cpp:187:14: warning: variable ‘gapCol’ set but not used [-Wunused-but-set-variable] 187 | bool gapCol; | ^~~~~~ sequenceContainer.cpp: In member function ‘void sequenceContainer::removeGapPositionsAllSeqs()’: sequenceContainer.cpp:199:14: warning: variable ‘gapCol’ set but not used [-Wunused-but-set-variable] 199 | bool gapCol; | ^~~~~~ sequenceContainer.cpp: In member function ‘int sequenceContainer::getNumOfOccurancesPerPos(int, char)’: sequenceContainer.cpp:452:19: warning: unused variable ‘len’ [-Wunused-variable] 452 | const int len = _seqDataVec[0].seqLen(); | ^~~ sequenceContainer.cpp: In member function ‘std::vector > sequenceContainer::getSeqNamesThatMatchPos(int, char)’: sequenceContainer.cpp:467:19: warning: unused variable ‘len’ [-Wunused-variable] 467 | const int len = _seqDataVec[0].seqLen(); | ^~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateTree.o simulateTree.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o siteSpecificRate.o siteSpecificRate.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o someUtil.o someUtil.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o split.o split.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitMap.o splitMap.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o splitTreeUtil.o splitTreeUtil.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcess.o stochasticProcess.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatComponent.o suffStatComponent.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o talRandom.o talRandom.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tree.o tree.cpp tree.cpp: In constructor ‘tree::tree(const std::string&)’: tree.cpp:180:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 180 | if (in.is_open()) | ^~ tree.cpp:182:17: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 182 | create_names_to_internal_nodes(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeIt.o treeIt.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o treeUtil.o treeUtil.cpp treeUtil.cpp: In function ‘std::vector getNexusTreesFromFile(const std::string&)’: treeUtil.cpp:371:32: warning: variable ‘itStrStart’ set but not used [-Wunused-but-set-variable] 371 | string::const_iterator itStrStart = it->begin(); | ^~~~~~~~~~ treeUtil.cpp:372:32: warning: variable ‘itStrEnd’ set but not used [-Wunused-but-set-variable] 372 | string::const_iterator itStrEnd = it->end(); | ^~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniDistribution.o uniDistribution.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o uniformDistribution.o uniformDistribution.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GLaguer.o GLaguer.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp In file included from distanceBasedSeqs2Tree.cpp:12: bestGtrModelParams.h: In constructor ‘C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)’: bestGtrModelParams.h:175:28: warning: ‘C_evalGTRParamProportional::_sp’ will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ bestGtrModelParams.h:173:34: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o posteriorDistance.o posteriorDistance.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp 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, | ^~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o doubleRep.o doubleRep.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o logRep.o logRep.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indel.o indel.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o indelModel.o indelModel.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mulAlphabet.o mulAlphabet.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o replacementModelSSRV.o replacementModelSSRV.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o matrixUtils.o matrixUtils.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaUtilities.o betaUtilities.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistribution.o betaDistribution.cpp In file included from betaDistribution.cpp:3: betaDistribution.h: In copy constructor ‘betaDistribution::betaDistribution(const betaDistribution&)’: betaDistribution.h:54:25: warning: ‘betaDistribution::_boundary’ will be initialized after [-Wreorder] 54 | vector _boundary; | ^~~~~~~~~ betaDistribution.h:47:17: warning: ‘double betaDistribution::_alpha’ [-Wreorder] 47 | MDOUBLE _alpha; | ^~~~~~ betaDistribution.cpp:23:1: warning: when initialized here [-Wreorder] 23 | betaDistribution::betaDistribution(const betaDistribution& other) : | ^~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o geneticCodeHolder.o geneticCodeHolder.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o samplingSequences.o samplingSequences.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2USSRV.o bblEM2USSRV.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestParamUSSRV.o bestParamUSSRV.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2USSRV.o likeDist2USSRV.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ussrvModel.o ussrvModel.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o normalDist.o normalDist.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o tamura92.o tamura92.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestTamura92param.o bestTamura92param.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o extremeValDistribution.o extremeValDistribution.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp 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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp 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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o distributionPlusCategory.o distributionPlusCategory.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateJumps.o simulateJumps.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o computeJumps.o computeJumps.cpp In file included from computeJumps.cpp:1: computeJumps.h: In constructor ‘computeJumps::gFunc::gFunc(double, double, double)’: computeJumps.h:59:25: warning: ‘computeJumps::gFunc::_Lambda2’ will be initialized after [-Wreorder] 59 | MDOUBLE _Lambda2; | ^~~~~~~~ computeJumps.h:57:25: warning: ‘double computeJumps::gFunc::_r’ [-Wreorder] 57 | MDOUBLE _r; | ^~ computeJumps.cpp:256:1: warning: when initialized here [-Wreorder] 256 | computeJumps::gFunc::gFunc(const MDOUBLE Lambda1, const MDOUBLE Lambda2 , const MDOUBLE r) | ^~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o seqeuncesFilter.o seqeuncesFilter.cpp seqeuncesFilter.cpp: In static member function ‘static void seqeuncesFilter::removeShortAndLongSequences(sequenceContainer&, int, int)’: seqeuncesFilter.cpp:141:25: warning: unused variable ‘pAlph’ [-Wunused-variable] 141 | const alphabet* pAlph = sc.getAlphabet(); | ^~~~~ In file included from 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; | ^~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureLS.o optGammaMixtureLS.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o mixtureDistribution.o mixtureDistribution.cpp 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/powerpc64le-linux-gnu/include/c++/13/powerpc64le-linux-gnu/bits/c++allocator.h:33, from /usr/powerpc64le-linux-gnu/include/c++/13/bits/allocator.h:46, from /usr/powerpc64le-linux-gnu/include/c++/13/vector:63, 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/powerpc64le-linux-gnu/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]’ at /usr/powerpc64le-linux-gnu/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’ at mixtureDistribution.cpp:84:24: /usr/powerpc64le-linux-gnu/include/c++/13/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 file included from /usr/powerpc64le-linux-gnu/include/c++/13/vector:66: 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/powerpc64le-linux-gnu/include/c++/13/bits/stl_vector.h:1289:28: warning: ‘pComp’ may be used uninitialized [-Wmaybe-uninitialized] 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/13/vector:72: /usr/powerpc64le-linux-gnu/include/c++/13/bits/vector.tcc: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’: /usr/powerpc64le-linux-gnu/include/c++/13/bits/vector.tcc:445:7: note: by argument 3 of type ‘generalGammaDistribution* const&’ to ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*; _Alloc = std::allocator]’ declared here 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:72:43: note: ‘pComp’ declared here 72 | 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/powerpc64le-linux-gnu/include/c++/13/bits/alloc_traits.h:538:17, inlined from ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator]’ at /usr/powerpc64le-linux-gnu/include/c++/13/bits/stl_vector.h:1283:30, inlined from ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’ at mixtureDistribution.cpp:52:24: /usr/powerpc64le-linux-gnu/include/c++/13/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 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/powerpc64le-linux-gnu/include/c++/13/bits/stl_vector.h:1289:28: warning: ‘pComp’ may be used uninitialized [-Wmaybe-uninitialized] 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/13/bits/vector.tcc: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’: /usr/powerpc64le-linux-gnu/include/c++/13/bits/vector.tcc:445:7: note: by argument 3 of type ‘generalGammaDistribution* const&’ to ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*; _Alloc = std::allocator]’ declared here 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ mixtureDistribution.cpp:40:43: note: ‘pComp’ declared here 40 | generalGammaDistribution* pComp; | ^~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp suffStatGammaMixture.cpp: In member function ‘void suffStatGammaMixture::computeStatistics()’: suffStatGammaMixture.cpp:123:33: warning: variable ‘Exp_Rk’ set but not used [-Wunused-but-set-variable] 123 | MDOUBLE Exp_Rk, Exp_LogRk, sum; | ^~~~~~ suffStatGammaMixture.cpp: In member function ‘double suffStatGammaMixture::computeQ()’: suffStatGammaMixture.cpp:224:25: warning: unused variable ‘first’ [-Wunused-variable] 224 | MDOUBLE first = _MkVec[comp] * log(P_k); | ^~~~~ suffStatGammaMixture.cpp:225:25: warning: unused variable ‘second’ [-Wunused-variable] 225 | MDOUBLE second = _MkVec[comp] * alpha_k*log(beta_k); | ^~~~~~ suffStatGammaMixture.cpp:226:25: warning: unused variable ‘third’ [-Wunused-variable] 226 | MDOUBLE third = -_MkVec[comp] * gammln(alpha_k); | ^~~~~ suffStatGammaMixture.cpp:227:25: warning: unused variable ‘fourth’ [-Wunused-variable] 227 | MDOUBLE fourth = -_AkVec[comp]*beta_k; | ^~~~~~ suffStatGammaMixture.cpp:228:25: warning: unused variable ‘fifth’ [-Wunused-variable] 228 | MDOUBLE fifth = _BkVec[comp]*(alpha_k-1.0); | ^~~~~ suffStatGammaMixture.cpp:216:17: warning: variable ‘res2’ set but not used [-Wunused-but-set-variable] 216 | MDOUBLE res2 = 0.0; | ^~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o GamMixtureOptimizer.o GamMixtureOptimizer.cpp In file included from GamMixtureOptimizer.cpp:3: optGammaMixtureEM.h: In member function ‘double C_evalAlphaEM::diGammaPlus(double) const’: optGammaMixtureEM.h:76:25: warning: unused variable ‘res1’ [-Wunused-variable] 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); | ^~~~ optGammaMixtureEM.h: In member function ‘double C_evalAlphaEM::diGamma(double) const’: optGammaMixtureEM.h:87:25: warning: unused variable ‘debugRes’ [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp In file included from optGammaMixtureEM.cpp:1: optGammaMixtureEM.h: In member function ‘double C_evalAlphaEM::diGammaPlus(double) const’: optGammaMixtureEM.h:76:25: warning: unused variable ‘res1’ [-Wunused-variable] 76 | MDOUBLE res1 = log(x) + (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))); | ^~~~ optGammaMixtureEM.h: In member function ‘double C_evalAlphaEM::diGamma(double) const’: optGammaMixtureEM.h:87:25: warning: unused variable ‘debugRes’ [-Wunused-variable] 87 | MDOUBLE debugRes = log(x) - (1/(2*x)) - (1/(12*x*x)) + (1/(120*pow(x, 4))) - (1/(252*pow(x, 6))) + (1/(240*pow(x, 8))) - (1/(132*pow(x, 10))); | ^~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gainLossAlphabet.o gainLossAlphabet.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o wYangModel.o wYangModel.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o codonUtils.o codonUtils.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likeDist2Codon.o likeDist2Codon.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o unObservableData.o unObservableData.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateModel.o threeStateModel.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o threeStateAlphabet.o threeStateAlphabet.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bblEM2codon.o bblEM2codon.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestAlphaAndK.o bestAlphaAndK.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o gtrModel.o gtrModel.cpp In file included from gtrModel.cpp:1: gtrModel.h: In constructor ‘gtrModel::gtrModel(const Vdouble&, double, double, double, double, double, double)’: gtrModel.h:54:17: warning: ‘gtrModel::_g2t’ will be initialized after [-Wreorder] 54 | MDOUBLE _g2t; | ^~~~ gtrModel.h:47:17: warning: ‘Vdouble gtrModel::_freq’ [-Wreorder] 47 | Vdouble _freq; | ^~~~~ gtrModel.cpp:5:1: warning: when initialized here [-Wreorder] 5 | gtrModel::gtrModel(const Vdouble& freq, | ^~~~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_a2c() const’: gtrModel.cpp:139:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 139 | return result; | ^~~~~~ gtrModel.cpp:130:17: note: ‘result’ was declared here 130 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_a2g() const’: gtrModel.cpp:153:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 153 | return result; | ^~~~~~ gtrModel.cpp:144:17: note: ‘result’ was declared here 144 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_a2t() const’: gtrModel.cpp:167:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 167 | return result; | ^~~~~~ gtrModel.cpp:158:17: note: ‘result’ was declared here 158 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_c2g() const’: gtrModel.cpp:181:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 181 | return result; | ^~~~~~ gtrModel.cpp:172:17: note: ‘result’ was declared here 172 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_c2t() const’: gtrModel.cpp:195:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 195 | return result; | ^~~~~~ gtrModel.cpp:186:17: note: ‘result’ was declared here 186 | MDOUBLE result; | ^~~~~~ gtrModel.cpp: In member function ‘double gtrModel::get_g2t() const’: gtrModel.cpp:209:16: warning: ‘result’ may be used uninitialized [-Wmaybe-uninitialized] 209 | return result; | ^~~~~~ gtrModel.cpp:200:17: note: ‘result’ was declared here 200 | MDOUBLE result; | ^~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o bestGtrModelParams.o bestGtrModelParams.cpp In file included from bestGtrModelParams.cpp:3: bestGtrModelParams.h: In constructor ‘C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)’: bestGtrModelParams.h:175:28: warning: ‘C_evalGTRParamProportional::_sp’ will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ bestGtrModelParams.h:173:34: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -DLOG -c -o integerAlphabet.o integerAlphabet.cpp ar rv libEvolTree.a AddLog.o NNiProp.o NNiSep.o Nni.o aaJC.o allTrees.o allTreesSeparateModel.o alphabet.o amino.o bestAlpha.o bestAlphaManyTrees.o bestHKYparam.o bootstrap.o bblEM.o bblEMfixRoot.o bblEMProprtional.o bblEMProportionalEB.o bblLSProportionalEB.o bblEMSeperate.o chebyshevAccelerator.o clustalFormat.o codon.o codonJC.o computeCounts.o computeDownAlg.o computeMarginalAlg.o computePijComponent.o computeUpAlg.o computeUpAlgFactors.o computeSubstitutionCounts.o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o ConversionUtils.o countTableComponent.o datMatrixHolder.o distanceTable.o distribution.o errorMsg.o evaluateCharacterFreq.o fastStartTree.o fastaFormat.o findRateOfGene.o fromCountTableComponentToDistance.o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistancePropEB.o fromQtoPt.o generalGammaDistributionFixedCategories.o gammaDistribution.o gammaUtilities.o generalGammaDistribution.o getRandomWeights.o goldmanYangModel.o granthamChemicalDistances.o hky.o simulateWithDependence.o KH_calculation.o likeDist.o likeDistfixRoot.o likeDistProp.o likeDistPropEB.o likelihoodComputation.o likelihoodComputationFactors.o logFile.o maseFormat.o molphyFormat.o nexusFormat.o nj.o njConstrain.o nucJC.o nucleotide.o numRec.o Parameters.o phylipFormat.o pijAccelerator.o readDatMatrix.o readTree.o recognizeFormat.o replacementModel.o searchStatus.o seqContainerTreeMap.o sequence.o sequenceContainer.o simulateTree.o siteSpecificRate.o someUtil.o split.o splitMap.o splitTreeUtil.o stochasticProcess.o suffStatComponent.o talRandom.o tree.o treeIt.o treeUtil.o uniDistribution.o uniformDistribution.o cmdline2EvolObjs.o generalGammaDistributionLaguerre.o gammaDistributionLaguerre.o GLaguer.o givenRatesMLDistance.o distanceBasedSeqs2Tree.o posteriorDistance.o pairwiseGammaDistance.o doubleRep.o logRep.o indel.o indelModel.o mulAlphabet.o replacementModelSSRV.o stochasticProcessSSRV.o bestAlphaAndNu.o C_evalParamUSSRV.o matrixUtils.o betaOmegaDistribution.o betaUtilities.o betaDistribution.o geneticCodeHolder.o samplingSequences.o bblEM2USSRV.o bestParamUSSRV.o likeDist2USSRV.o ussrvModel.o likelihoodComputation2USSRV.o fromCountTableComponentToDistance2USSRV.o normalDist.o tamura92.o bestTamura92param.o phylipSequentialFormat.o simulateCodonsJumps.o simulateJumpsAbstract.o ssrvDistanceSeqs2Tree.o multipleStochasticProcess.o distributionPlusInvariant.o extremeValDistribution.o gammaDistributionFixedCategories.o generalGammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.o distributionPlusCategory.o simulateJumps.o computeJumps.o seqeuncesFilter.o optGammaMixtureLS.o mixtureDistribution.o suffStatGammaMixture.o GamMixtureOptimizer.o optGammaMixtureEM.o gainLossAlphabet.o wYangModel.o codonUtils.o likelihoodComputation2Codon.o likeDist2Codon.o unObservableData.o likelihoodComputationGL.o threeStateModel.o threeStateAlphabet.o oneTwoMoreModel.o betaDistributionFixedCategories.o betaDistributionFixedCategoriesWithOmegaUniform.o bblEM2codon.o bestAlphaAndK.o fromCountTableComponentToDistance2Codon.o gtrModel.o bestGtrModelParams.o simulateRateShiftJumps.o integerAlphabet.o ar: creating libEvolTree.a a - AddLog.o a - NNiProp.o a - NNiSep.o a - Nni.o a - aaJC.o a - allTrees.o a - allTreesSeparateModel.o a - alphabet.o a - amino.o a - bestAlpha.o a - bestAlphaManyTrees.o a - bestHKYparam.o a - bootstrap.o a - bblEM.o a - bblEMfixRoot.o a - bblEMProprtional.o a - bblEMProportionalEB.o a - bblLSProportionalEB.o a - bblEMSeperate.o a - chebyshevAccelerator.o a - clustalFormat.o a - codon.o a - codonJC.o a - computeCounts.o a - computeDownAlg.o a - computeMarginalAlg.o a - computePijComponent.o a - computeUpAlg.o a - computeUpAlgFactors.o a - computeSubstitutionCounts.o a - computePosteriorExpectationOfSubstitutions.o a - computePosteriorExpectationOfSubstitutions_nonReversibleSp.o a - ConversionUtils.o a - countTableComponent.o a - datMatrixHolder.o a - distanceTable.o a - distribution.o a - errorMsg.o a - evaluateCharacterFreq.o a - fastStartTree.o a - fastaFormat.o a - findRateOfGene.o a - fromCountTableComponentToDistance.o a - fromCountTableComponentToDistancefixRoot.o a - fromCountTableComponentToDistanceProp.o a - fromCountTableComponentToDistancePropEB.o a - fromQtoPt.o a - generalGammaDistributionFixedCategories.o a - gammaDistribution.o a - gammaUtilities.o a - generalGammaDistribution.o a - getRandomWeights.o a - goldmanYangModel.o a - granthamChemicalDistances.o a - hky.o a - simulateWithDependence.o a - KH_calculation.o a - likeDist.o a - likeDistfixRoot.o a - likeDistProp.o a - likeDistPropEB.o a - likelihoodComputation.o a - likelihoodComputationFactors.o a - logFile.o a - maseFormat.o a - molphyFormat.o a - nexusFormat.o a - nj.o a - njConstrain.o a - nucJC.o a - nucleotide.o a - numRec.o a - Parameters.o a - phylipFormat.o a - pijAccelerator.o a - readDatMatrix.o a - readTree.o a - recognizeFormat.o a - replacementModel.o a - searchStatus.o a - seqContainerTreeMap.o a - sequence.o a - sequenceContainer.o a - simulateTree.o a - siteSpecificRate.o a - someUtil.o a - split.o a - splitMap.o a - splitTreeUtil.o a - stochasticProcess.o a - suffStatComponent.o a - talRandom.o a - tree.o a - treeIt.o a - treeUtil.o a - uniDistribution.o a - uniformDistribution.o a - cmdline2EvolObjs.o a - generalGammaDistributionLaguerre.o a - gammaDistributionLaguerre.o a - GLaguer.o a - givenRatesMLDistance.o a - distanceBasedSeqs2Tree.o a - posteriorDistance.o a - pairwiseGammaDistance.o a - doubleRep.o a - logRep.o a - indel.o a - indelModel.o a - mulAlphabet.o a - replacementModelSSRV.o a - stochasticProcessSSRV.o a - bestAlphaAndNu.o a - C_evalParamUSSRV.o a - matrixUtils.o a - betaOmegaDistribution.o a - betaUtilities.o a - betaDistribution.o a - geneticCodeHolder.o a - samplingSequences.o a - bblEM2USSRV.o a - bestParamUSSRV.o a - likeDist2USSRV.o a - ussrvModel.o a - likelihoodComputation2USSRV.o a - fromCountTableComponentToDistance2USSRV.o a - normalDist.o a - tamura92.o a - bestTamura92param.o a - phylipSequentialFormat.o a - simulateCodonsJumps.o a - simulateJumpsAbstract.o a - ssrvDistanceSeqs2Tree.o a - multipleStochasticProcess.o a - distributionPlusInvariant.o a - extremeValDistribution.o a - gammaDistributionFixedCategories.o a - generalGammaDistributionPlusInvariant.o a - gammaDistributionPlusInvariant.o a - distributionPlusCategory.o a - simulateJumps.o a - computeJumps.o a - seqeuncesFilter.o a - optGammaMixtureLS.o a - mixtureDistribution.o a - suffStatGammaMixture.o a - GamMixtureOptimizer.o a - optGammaMixtureEM.o a - gainLossAlphabet.o a - wYangModel.o a - codonUtils.o a - likelihoodComputation2Codon.o a - likeDist2Codon.o a - unObservableData.o a - likelihoodComputationGL.o a - threeStateModel.o a - threeStateAlphabet.o a - oneTwoMoreModel.o a - betaDistributionFixedCategories.o a - betaDistributionFixedCategoriesWithOmegaUniform.o a - bblEM2codon.o a - bestAlphaAndK.o a - fromCountTableComponentToDistance2Codon.o a - gtrModel.o a - bestGtrModelParams.o a - simulateRateShiftJumps.o a - integerAlphabet.o ranlib libEvolTree.a make[3]: Leaving directory '/<>/libs/phylogeny' make[2]: Leaving directory '/<>/libs' cd programs;make all make[2]: Entering directory '/<>/programs' cd fastml && make all make[3]: Entering directory '/<>/programs/fastml' making depend powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o fastml.o fastml.cpp In file included from bbAlg.h:8, from fastml.cpp:254: bbReport.h: In constructor ‘BandBReportAllPos::BandBReportAllPos(const std::string&, int)’: bbReport.h:14:23: warning: ‘BandBReportAllPos::_reportFileName’ will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ In file included from mainbb.h:4, from fastml.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbAlg.o bbAlg.cpp In file included from bbAlg.h:8, from bbAlg.cpp:1: bbReport.h: In constructor ‘BandBReportAllPos::BandBReportAllPos(const std::string&, int)’: bbReport.h:14:23: warning: ‘BandBReportAllPos::_reportFileName’ will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ bbAlg.h: In constructor ‘bbAlg::bbAlg(const tree&, std::vector&, const sequenceContainer&, boundMethod, const std::string&, double, const distribution*)’: bbAlg.h:61:23: warning: ‘bbAlg::_reportFileName’ will be initialized after [-Wreorder] 61 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbAlg.h:60:27: warning: ‘BandBReportAllPos bbAlg::BandBReportAllPos1’ [-Wreorder] 60 | BandBReportAllPos BandBReportAllPos1; // report for all positions. | ^~~~~~~~~~~~~~~~~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(const tree& et, | ^~~~~ bbAlg.h:60:27: warning: ‘bbAlg::BandBReportAllPos1’ will be initialized after [-Wreorder] 60 | BandBReportAllPos BandBReportAllPos1; // report for all positions. | ^~~~~~~~~~~~~~~~~~ bbAlg.h:29:21: warning: ‘const tree& bbAlg::_et’ [-Wreorder] 29 | const tree& _et; | ^~~ bbAlg.cpp:7:1: warning: when initialized here [-Wreorder] 7 | bbAlg::bbAlg(const tree& et, | ^~~~~ In file included from bbNodeOrderAlg.h:5, from bbAlg.h:5: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.cpp In file included from bbEvaluateSpecificAV.cpp:1: bbEvaluateSpecificAV.h: In constructor ‘bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&)’: bbEvaluateSpecificAV.h:34:34: warning: ‘bbEvaluateSpecificAV::_sc’ will be initialized after [-Wreorder] 34 | const sequenceContainer& _sc; | ^~~ bbEvaluateSpecificAV.h:31:30: warning: ‘const computePijGam& bbEvaluateSpecificAV::_bbcpij’ [-Wreorder] 31 | const computePijGam& _bbcpij; | ^~~~~~~ bbEvaluateSpecificAV.cpp:3:1: warning: when initialized here [-Wreorder] 3 | bbEvaluateSpecificAV::bbEvaluateSpecificAV(const tree& et, | ^~~~~~~~~~~~~~~~~~~~ bbEvaluateSpecificAV.cpp: In member function ‘double bbEvaluateSpecificAV::recursiveEvaluateSpecificAv(int, tree::nodeP, int)’: bbEvaluateSpecificAV.cpp:65:33: warning: unused variable ‘rate’ [-Wunused-variable] 65 | MDOUBLE rate = _sp.rates(categor); // the r. | ^~~~ In file included from bbEvaluateSpecificAV.h:4: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp In file included from bbfindBestAVDynProg.h:5, from bbfindBestAVDynProg.cpp:1: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp In file included from bbNodeOrderAlg.cpp:1: bbNodeOrderAlg.h: In constructor ‘bbNodeOrderAlg::bbNodeOrderAlg(const tree&, const stochasticProcess&, const sequenceContainer&, const computePijGam&, double)’: bbNodeOrderAlg.h:33:34: warning: ‘bbNodeOrderAlg::_sc’ will be initialized after [-Wreorder] 33 | const sequenceContainer& _sc; | ^~~ bbNodeOrderAlg.h:32:30: warning: ‘const computePijGam& bbNodeOrderAlg::_cpij’ [-Wreorder] 32 | const computePijGam& _cpij; | ^~~~~ bbNodeOrderAlg.cpp:8:1: warning: when initialized here [-Wreorder] 8 | bbNodeOrderAlg::bbNodeOrderAlg(const tree& et, | ^~~~~~~~~~~~~~ In file included from bbNodeOrderAlg.h:5: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bb_options.o bb_options.cpp In file included from bb_options.cpp:2: bb_options.h: In constructor ‘bb_options::bb_options(int&, char**)’: bb_options.h:49:16: warning: ‘bb_options::reportFile’ will be initialized after [-Wreorder] 49 | string reportFile; | ^~~~~~~~~~ bb_options.h:44:16: warning: ‘std::string bb_options::outFile_seq_joint’ [-Wreorder] 44 | string outFile_seq_joint; | ^~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:45:16: warning: ‘bb_options::outFile_seq_marginal’ will be initialized after [-Wreorder] 45 | string outFile_seq_marginal; | ^~~~~~~~~~~~~~~~~~~~ bb_options.h:42:16: warning: ‘std::string bb_options::outFile_prob_joint’ [-Wreorder] 42 | string outFile_prob_joint; | ^~~~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:43:16: warning: ‘bb_options::outFile_prob_marginal’ will be initialized after [-Wreorder] 43 | string outFile_prob_marginal; | ^~~~~~~~~~~~~~~~~~~~~ bb_options.h:24:16: warning: ‘std::string bb_options::seqfile’ [-Wreorder] 24 | string seqfile; | ^~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:30:28: warning: ‘bb_options::distributionName’ will be initialized after [-Wreorder] 30 | distributionsNames distributionName; | ^~~~~~~~~~~~~~~~ bb_options.h:26:23: warning: ‘bb_options::SeqFileFormat bb_options::seqOutputFormat’ [-Wreorder] 26 | SeqFileFormat seqOutputFormat; | ^~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:41:16: warning: ‘bb_options::outTreeFileAncestor’ will be initialized after [-Wreorder] 41 | string outTreeFileAncestor; | ^~~~~~~~~~~~~~~~~~~ bb_options.h:32:22: warning: ‘bb_options::boundMethods bb_options::boundMethod’ [-Wreorder] 32 | boundMethods boundMethod; | ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:47:17: warning: ‘bb_options::gammaPar’ will be initialized after [-Wreorder] 47 | MDOUBLE gammaPar; | ^~~~~~~~ bb_options.h:28:14: warning: ‘bool bb_options::userProvideAlpha’ [-Wreorder] 28 | bool userProvideAlpha; | ^~~~~~~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:48:13: warning: ‘bb_options::gammaCategies’ will be initialized after [-Wreorder] 48 | int gammaCategies; | ^~~~~~~~~~~~~ bb_options.h:36:26: warning: ‘bb_options::modelNameOptions bb_options::modelName’ [-Wreorder] 36 | modelNameOptions modelName; | ^~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h:39:14: warning: ‘bb_options::useChebyshev’ will be initialized after [-Wreorder] 39 | bool useChebyshev; | ^~~~~~~~~~~~ bb_options.h:27:16: warning: ‘std::string bb_options::treeOutFile’ [-Wreorder] 27 | string treeOutFile; | ^~~~~~~~~~~ bb_options.cpp:6:1: warning: when initialized here [-Wreorder] 6 | bb_options::bb_options(int& argc, char *argv[]): | ^~~~~~~~~~ bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bbReport.o bbReport.cpp In file included from bbReport.cpp:1: bbReport.h: In constructor ‘BandBReportAllPos::BandBReportAllPos(const std::string&, int)’: bbReport.h:14:23: warning: ‘BandBReportAllPos::_reportFileName’ will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ bbReport.h: In constructor ‘BandBReport::BandBReport(const std::string&, int, int)’: bbReport.h:53:23: warning: ‘BandBReport::_reportFileName’ will be initialized after [-Wreorder] 53 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:51:19: warning: ‘const int BandBReport::_position’ [-Wreorder] 51 | const int _position; | ^~~~~~~~~ bbReport.cpp:10:1: warning: when initialized here [-Wreorder] 10 | BandBReport::BandBReport( const string& reportFileName, const int position, const int alphabetSize ) : | ^~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp computeMarginalReconstruction.cpp: In member function ‘void computeMarginalReconstruction::compute(const distribution*)’: computeMarginalReconstruction.cpp:67:25: warning: unused variable ‘likelihoodOfPos’ [-Wunused-variable] 67 | MDOUBLE likelihoodOfPos = 0; | ^~~~~~~~~~~~~~~ computeMarginalReconstruction.cpp:45:17: warning: unused variable ‘totalLikelihoodOfReconstruction’ [-Wunused-variable] 45 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o jointNoGamma.o jointNoGamma.cpp jointNoGamma.cpp: In member function ‘void jointNoGamma::compute()’: jointNoGamma.cpp:23:17: warning: unused variable ‘totalLikelihoodOfReconstruction’ [-Wunused-variable] 23 | MDOUBLE totalLikelihoodOfReconstruction = 0; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ jointNoGamma.cpp: In member function ‘std::vector jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)’: jointNoGamma.cpp:108:33: warning: unused variable ‘maxL’ [-Wunused-variable] 108 | MDOUBLE maxL = VERYSMALL; | ^~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o mainbb.o mainbb.cpp In file included from bbAlg.h:8, from mainbb.cpp:5: bbReport.h: In constructor ‘BandBReportAllPos::BandBReportAllPos(const std::string&, int)’: bbReport.h:14:23: warning: ‘BandBReportAllPos::_reportFileName’ will be initialized after [-Wreorder] 14 | const string& _reportFileName; | ^~~~~~~~~~~~~~~ bbReport.h:13:19: warning: ‘const int BandBReportAllPos::_minNumOfNodesToVisit’ [-Wreorder] 13 | const int _minNumOfNodesToVisit; | ^~~~~~~~~~~~~~~~~~~~~ bbReport.h:10:18: warning: when initialized here [-Wreorder] 10 | explicit BandBReportAllPos(const string& reportFileName, int minNumOfNodesToVisit) | ^~~~~~~~~~~~~~~~~ In file included from mainbb.cpp:31: ../../libs/phylogeny/bestGtrModelParams.h: In constructor ‘C_evalGTRParamProportional::C_evalGTRParamProportional(GTRParam, const tree&, const sequenceContainer&, stochasticProcess&, const gammaDistribution*, const Vdouble*)’: ../../libs/phylogeny/bestGtrModelParams.h:175:28: warning: ‘C_evalGTRParamProportional::_sp’ will be initialized after [-Wreorder] 175 | stochasticProcess& _sp; | ^~~ ../../libs/phylogeny/bestGtrModelParams.h:173:34: warning: ‘const gammaDistribution* C_evalGTRParamProportional::_pProportionDist’ [-Wreorder] 173 | const gammaDistribution* _pProportionDist; | ^~~~~~~~~~~~~~~~ ../../libs/phylogeny/bestGtrModelParams.h:162:3: warning: when initialized here [-Wreorder] 162 | C_evalGTRParamProportional( const GTRParam param, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mainbb.h:4, from mainbb.cpp:1: bb_options.h: At global scope: bb_options.h:62:21: warning: ‘const std::string usege_splash_screen()’ defined but not used [-Wunused-function] 62 | static const string usege_splash_screen() { | ^~~~~~~~~~~~~~~~~~~ mainbb.cpp: In member function ‘void mainbb::findAncestralSequencesGammaJoint()’: mainbb.cpp:428:108: warning: ‘bm’ may be used uninitialized [-Wmaybe-uninitialized] 428 | bbAlg bbAlg1(_et,_spVec,_sc,bm,_options->reportFile,_options->computeAgainExactTreshold,_forceDistr); | ^ mainbb.cpp:423:28: note: ‘bm’ was declared here 423 | bbAlg::boundMethod bm; | ^~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sequenceDataDiff.o sequenceDataDiff.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp ar rv libfastml.a fastml.o bbAlg.o bbComputeDownAlg.o bbComputeUpAlg.o bbEvaluateSpecificAV.o bbfindBestAVDynProg.o bbNodeOrderAlg.o bb_options.o bbReport.o computeMarginalReconstruction.o jointNoGamma.o mainbb.o sequenceDataDiff.o suffStatComponentJointNoGamma.o ar: creating libfastml.a a - fastml.o a - bbAlg.o a - bbComputeDownAlg.o a - bbComputeUpAlg.o a - bbEvaluateSpecificAV.o a - bbfindBestAVDynProg.o a - bbNodeOrderAlg.o a - bb_options.o a - bbReport.o a - computeMarginalReconstruction.o a - jointNoGamma.o a - mainbb.o a - sequenceDataDiff.o a - suffStatComponentJointNoGamma.o ranlib libfastml.a powerpc64le-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml make[3]: Leaving directory '/<>/programs/fastml' cd gainLoss && make all make[3]: Entering directory '/<>/programs/gainLoss' making depend powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp gainLossOptions.cpp: In static member function ‘static gainLossOptions::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; | ^~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss.o gainLoss.cpp In file included from gainLoss.h: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: 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/powerpc64le-linux-gnu/include/c++/13/iostream:41, 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘AlphaRate’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘Loss’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘Theta’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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::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::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::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; | ^~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossUtils.o gainLossUtils.cpp In file included from ../../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: 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; | ^~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp In file included from ../../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: 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; | ^~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.cpp In file included from ../../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: 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; | ^~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossModel.o gainLossModel.cpp In file included from ../../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: 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): | ^~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o siteSpecificGL.o siteSpecificGL.cpp In file included from ../../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: 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computePosteriorExpectationOfChange.o computePosteriorExpectationOfChange.cpp In file included from ../../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: 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/powerpc64le-linux-gnu/include/c++/13/iostream:41, 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘Down’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘Up’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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/powerpc64le-linux-gnu/include/c++/13/ostream:223:25: warning: ‘pij’ may be used uninitialized [-Wmaybe-uninitialized] 223 | { 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; | ^~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossProject.o gainLossProject.cpp In file included from gainLoss.h: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: 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptimizer.o gainLossOptimizer.cpp In file included from gainLoss.h: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: 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; | ^~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o rate4siteGL.o rate4siteGL.cpp In file included from gainLoss.h: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: 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; | ^~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCountsGL.o computeCountsGL.cpp In file included from gainLoss.h: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: 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): | ^~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o computeCorrelations.o computeCorrelations.cpp In file included from gainLoss.h: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: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘void computeCorrelations::runComputeCorrelations(const Vint&, const Vint&, bool)’: computeCorrelations.cpp:130:13: warning: unused variable ‘numOfbranches’ [-Wunused-variable] 130 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node | ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)’: computeCorrelations.cpp:408:29: warning: unused variable ‘isHigherNminReducedFreqOfHighCorr’ [-Wunused-variable] 408 | int isHigherNminReducedFreqOfHighCorr = false; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:348:21: warning: unused variable ‘typeIndex’ [-Wunused-variable] 348 | int typeIndex = corIndex % _EventTypes.size(); // in case both Spearman and pearson are used | ^~~~~~~~~ computeCorrelations.cpp: In member function ‘void computeCorrelations::printCorrelationsFrequencies(Vdouble&, std::ofstream*)’: computeCorrelations.cpp:559:30: warning: NULL used in arithmetic [-Wpointer-arith] 559 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:569:38: warning: NULL used in arithmetic [-Wpointer-arith] 569 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:579:38: warning: NULL used in arithmetic [-Wpointer-arith] 579 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp:584:30: warning: NULL used in arithmetic [-Wpointer-arith] 584 | if(!simCorrelStream==NULL) | ^~~~ computeCorrelations.cpp: In member function ‘int computeCorrelations::computedCorrelationsPValBasedOnSimulatedDataCoMapBins(VVVdouble&, std::vector >&, VVVVdouble&, VVVdouble&, std::map, std::map, double> > > >&, Vdouble&, Vint&, Vint&, Vint&, bool)’: computeCorrelations.cpp:676:37: warning: variable ‘prevNumberOfSimulationsInRange’ set but not used [-Wunused-but-set-variable] 676 | int prevNumberOfSimulationsInRange = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:677:37: warning: variable ‘prevNumberOfSimulationPointsMoreExtremeOrEqToCorr’ set but not used [-Wunused-but-set-variable] 677 | int prevNumberOfSimulationPointsMoreExtremeOrEqToCorr = 1; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:679:37: warning: unused variable ‘numOfBinsWithLowerSignificance’ [-Wunused-variable] 679 | int numOfBinsWithLowerSignificance = 0; // allow 2 "bin-iteration" even with lower significance to mitigate chance of "missing" higher significance in lower bin | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:680:38: warning: unused variable ‘isNextLowerBinAllowed’ [-Wunused-variable] 680 | bool isNextLowerBinAllowed = true; | ^~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘void computeCorrelations::produceSymeticMatrix(VVVdouble&, bool)’: computeCorrelations.cpp:894:26: warning: logical not is only applied to the left hand side of comparison [-Wlogical-not-parentheses] 894 | if(!numOfSites_A == numOfSites_B){ | ^~ computeCorrelations.cpp:894:12: note: add parentheses around left hand side expression to silence this warning 894 | if(!numOfSites_A == numOfSites_B){ | ^~~~~~~~~~~~~ | ( ) computeCorrelations.cpp: In member function ‘void computeCorrelations::printComputedCorrelations(const Vint&, const Vint&, bool, bool, VVVdouble*, std::string*)’: computeCorrelations.cpp:1009:14: warning: unused variable ‘isPearson’ [-Wunused-variable] 1009 | bool isPearson = false; | ^~~~~~~~~ computeCorrelations.cpp:1025:13: warning: unused variable ‘numOfbranches’ [-Wunused-variable] 1025 | int numOfbranches = _tr.getNodesNum()-1; // was -1, minus the root node | ^~~~~~~~~~~~~ computeCorrelations.cpp: In member function ‘VVVdouble computeCorrelations::pVals2qVals(VVVdouble&, std::map, std::map, double> > > >&, std::vector >&, Vdouble&, Vint&, Vint&)’: computeCorrelations.cpp:1347:67: warning: narrowing conversion of ‘gainLossOptions::_pValueCutOffForBootStrap’ from ‘double’ to ‘float’ [-Wnarrowing] 1347 | float pVals2checkBeforeFDR [] = {gainLossOptions::_pValueCutOffForBootStrap, 0.05, 0.01, 0.005, 0.001, 0.0001}; | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ computeCorrelations.cpp:1300:14: warning: variable ‘it_siteB’ set but not used [-Wunused-but-set-variable] 1300 | it_B it_siteB = it_siteA->second.begin(); | ^~~~~~~~ computeCorrelations.cpp: In member function ‘int computeCorrelations::produceSortedVectorsOfCorrelationsBinedByRate(double, std::ofstream*)’: computeCorrelations.cpp:505:33: warning: ‘expextedFreq’ may be used uninitialized [-Wmaybe-uninitialized] 505 | if(freqOfHighCorr>expextedFreq && freqOfHighCorr>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLoss4site.o gainLoss4site.cpp In file included from gainLoss.h:30, from gainLoss4site.h:24, from gainLoss4site.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: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ gainLoss4site.h: In constructor ‘gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector >, distribution*, distribution*, std::string&, unObservableData*, double)’: gainLoss4site.h:68:14: warning: ‘gainLoss4site::_tr’ will be initialized after [-Wreorder] 68 | tree _tr; | ^~~ gainLoss4site.h:61:45: warning: ‘std::vector > gainLoss4site::_spVVec’ [-Wreorder] 61 | vector > _spVVec; //save stochasticProcess for each category | ^~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ gainLoss4site.h:79:27: warning: ‘gainLoss4site::_unObservableData_p’ will be initialized after [-Wreorder] 79 | unObservableData* _unObservableData_p; // | ^~~~~~~~~~~~~~~~~~~ gainLoss4site.h:78:17: warning: ‘double gainLoss4site::_alphaConf’ [-Wreorder] 78 | MDOUBLE _alphaConf; | ^~~~~~~~~~ gainLoss4site.cpp:22:1: warning: when initialized here [-Wreorder] 22 | gainLoss4site::gainLoss4site(sequenceContainer& sc, tree& tr, | ^~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateChangesAlongTree.o simulateChangesAlongTree.cpp In file included from gainLoss.h:30, from simulateChangesAlongTree.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: 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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o simulateOnePos.o simulateOnePos.cpp In file included from gainLoss.h:30, from simulateOnePos.cpp:32: ../../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: In constructor ‘gainLossModelNonReversible::gainLossModelNonReversible(double, double, Vdouble, bool, bool, bool)’: gainLossModel.h:186:17: warning: ‘gainLossModelNonReversible::_loss’ will be initialized after [-Wreorder] 186 | MDOUBLE _loss; // _Q[1][0] | ^~~~~ gainLossModel.h:128:109: warning: base ‘gainLossModel’ [-Wreorder] 128 | :_loss(m2),gainLossModel(m1,freq,isRootFreqEQstationary,false,isHGT_normal_Pij,_isHGT_with_Q) | ^ gainLossModel.h:127:18: warning: when initialized here [-Wreorder] 127 | explicit gainLossModelNonReversible(const MDOUBLE m1, const MDOUBLE m2, const Vdouble freq,bool isRootFreqEQstationary, bool isHGT_normal_Pij, bool _isHGT_with_Q) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from simulateOnePos.cpp:18: simulateOnePos.h: In constructor ‘simulateOnePos::simulateOnePos(std::string, std::ostream*, std::ostream*, int, std::string, double, double, bool, stochasticProcess*, tree*, Vdouble*, Vdouble*)’: simulateOnePos.h:72:14: warning: ‘simulateOnePos::_simulateNullModel’ will be initialized after [-Wreorder] 72 | bool _simulateNullModel; | ^~~~~~~~~~~~~~~~~~ simulateOnePos.h:63:13: warning: ‘int simulateOnePos::_simNum’ [-Wreorder] 63 | int _simNum; | ^~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.h:65:17: warning: ‘simulateOnePos::_theta’ will be initialized after [-Wreorder] 65 | MDOUBLE _theta; | ^~~~~~ simulateOnePos.h:64:17: warning: ‘double simulateOnePos::_sumGainLoss’ [-Wreorder] 64 | MDOUBLE _sumGainLoss; | ^~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.h:75:18: warning: ‘simulateOnePos::_freq_cpN’ will be initialized after [-Wreorder] 75 | Vdouble* _freq_cpN; | ^~~~~~~~~ simulateOnePos.h:69:18: warning: ‘std::ostream* simulateOnePos::_simulatedEvents’ [-Wreorder] 69 | ostream *_simulatedEvents; | ^~~~~~~~~~~~~~~~ simulateOnePos.cpp:40:1: warning: when initialized here [-Wreorder] 40 | simulateOnePos::simulateOnePos(string simSeqFile, ostream* resFile, ostream* simulatedEvents, int simNum, string treeFile | ^~~~~~~~~~~~~~ simulateOnePos.cpp: In member function ‘void simulateOnePos::simulateOnePosLGT(stochasticProcess*, std::string)’: simulateOnePos.cpp:181:30: warning: unused variable ‘isRevers’ [-Wunused-variable] 181 | bool isRevers = false; | ^~~~~~~~ simulateOnePos.cpp:202:33: warning: variable ‘sumQii’ set but not used [-Wunused-but-set-variable] 202 | MDOUBLE sumQii = 1.0; | ^~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o bblLS.o bblLS.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from bblLS.h:27, from bblLS.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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bblLS.h:50:31: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 50 | MDOUBLE curL =NULL); | ^~~~ bblLS.h:58:31: warning: converting to non-pointer type ‘double’ from NULL [-Wconversion-null] 58 | MDOUBLE curL =NULL); | ^~~~ bblLS.h: In constructor ‘evalBranchSPvv::evalBranchSPvv(tree::nodeP, tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)’: bblLS.h:119:27: warning: ‘evalBranchSPvv::_unObservableData_p’ will be initialized after [-Wreorder] 119 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:118:18: warning: ‘Vdouble* evalBranchSPvv::_weights’ [-Wreorder] 118 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:96:18: warning: when initialized here [-Wreorder] 96 | explicit evalBranchSPvv(tree::nodeP pNode, tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~ bblLS.h: In constructor ‘evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector >&, const distribution*, const distribution*, Vdouble*, unObservableData*)’: bblLS.h:174:27: warning: ‘evalBranchProportionExponentSPvv::_unObservableData_p’ will be initialized after [-Wreorder] 174 | unObservableData* _unObservableData_p; | ^~~~~~~~~~~~~~~~~~~ bblLS.h:173:18: warning: ‘Vdouble* evalBranchProportionExponentSPvv::_weights’ [-Wreorder] 173 | Vdouble* _weights; | ^~~~~~~~ bblLS.h:152:18: warning: when initialized here [-Wreorder] 152 | explicit evalBranchProportionExponentSPvv(tree* tr, const sequenceContainer &sc, vector >& spVVec, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bblLS.cpp: In member function ‘double bblLS::optimizeBranches(tree&, stochasticProcess*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)’: bblLS.cpp:36:21: warning: NULL used in arithmetic [-Wpointer-arith] 36 | if (curL == NULL) | ^~~~ bblLS.cpp: In member function ‘double bblLS::optimizeBranches(tree&, std::vector >&, const distribution*, const distribution*, const sequenceContainer&, Vdouble*, unObservableData*, int, double, int, double)’: bblLS.cpp:112:21: warning: NULL used in arithmetic [-Wpointer-arith] 112 | if (curL == NULL) | ^~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o sankoffReconstructGL.o sankoffReconstructGL.cpp In file included from ../../libs/phylogeny/generalGammaDistributionPlusInvariant.h:9, from gainLossUtils.h:27, from sankoffReconstructGL.h:29, from sankoffReconstructGL.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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h: In constructor ‘sankoffReconstructGL::sankoffReconstructGL(sequenceContainer&, tree&, std::string&, double, double)’: sankoffReconstructGL.h:85:16: warning: ‘sankoffReconstructGL::_outDir’ will be initialized after [-Wreorder] 85 | string _outDir; | ^~~~~~~ sankoffReconstructGL.h:84:17: warning: ‘double sankoffReconstructGL::_costMatrixGainLossRatio’ [-Wreorder] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:84:17: warning: ‘sankoffReconstructGL::_costMatrixGainLossRatio’ will be initialized after [-Wreorder] 84 | MDOUBLE _costMatrixGainLossRatio; | ^~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.h:83:17: warning: ‘double sankoffReconstructGL::_distanceFromRootForRecent’ [-Wreorder] 83 | MDOUBLE _distanceFromRootForRecent; | ^~~~~~~~~~~~~~~~~~~~~~~~~~ sankoffReconstructGL.cpp:32:1: warning: when initialized here [-Wreorder] 32 | sankoffReconstructGL::sankoffReconstructGL(sequenceContainer& sc, tree& tr, string& outDir, MDOUBLE costMatrixGainLossRatio, MDOUBLE distanceFromRootForRecent): | ^~~~~~~~~~~~~~~~~~~~ ar rv libgainLoss.a gainLossOptions.o gainLoss.o gainLossUtils.o optimizeGainLossModel.o optimizeGainLossModelVV.o ../../libs/phylogeny/likelihoodComputationGL.o gainLossModel.o siteSpecificGL.o computePosteriorExpectationOfChange.o gainLossProject.o gainLossOptimizer.o ancestralReconstructStates.o rate4siteGL.o computeCountsGL.o computeCorrelations.o gainLoss4site.o simulateChangesAlongTree.o simulateOnePos.o bblLS.o sankoffReconstructGL.o ar: creating libgainLoss.a a - gainLossOptions.o a - gainLoss.o a - gainLossUtils.o a - optimizeGainLossModel.o a - optimizeGainLossModelVV.o a - ../../libs/phylogeny/likelihoodComputationGL.o a - gainLossModel.o a - siteSpecificGL.o a - computePosteriorExpectationOfChange.o a - gainLossProject.o a - gainLossOptimizer.o a - ancestralReconstructStates.o a - rate4siteGL.o a - computeCountsGL.o a - computeCorrelations.o a - gainLoss4site.o a - simulateChangesAlongTree.o a - simulateOnePos.o a - bblLS.o a - sankoffReconstructGL.o ranlib libgainLoss.a powerpc64le-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss make[3]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make all make[3]: Entering directory '/<>/programs/indelCoder' making depend powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoder.o indelCoder.cpp indelCoder.cpp: In member function ‘void indelCoder::printGapsInfo()’: indelCoder.cpp:422:13: warning: unused variable ‘gapNum’ [-Wunused-variable] 422 | int gapNum = 1; | ^~~~~~ indelCoder.cpp: In member function ‘void indelCoder::printIndelSummary()’: indelCoder.cpp:587:14: warning: unused variable ‘isSIC’ [-Wunused-variable] 587 | bool isSIC = indelCoderOptions::_codingType == indelCoderOptions::SIC; | ^~~~~ indelCoder.cpp:597:13: warning: unused variable ‘seqLeng’ [-Wunused-variable] 597 | int seqLeng = _sc.seqLen(); | ^~~~~~~ indelCoder.cpp: In member function ‘void indelCoder::delimitationOfCharacters(indelCoderOptions::codingType)’: indelCoder.cpp:175:33: warning: ‘condition’ may be used uninitialized [-Wmaybe-uninitialized] 175 | while(condition && _gaps[i]->getCoord3()>character_p->getCoord3() ){ | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ indelCoder.cpp:170:22: note: ‘condition’ was declared here 170 | bool condition; | ^~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderOptions.o indelCoderOptions.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderProject.o indelCoderProject.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o indelCoderUtils.o indelCoderUtils.cpp powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o character.o character.cpp character.cpp: In member function ‘int character::getLongestGapStIndex()’: character.cpp:28:16: warning: ‘longestGapStIndex’ may be used uninitialized [-Wmaybe-uninitialized] 28 | return longestGapStIndex; | ^~~~~~~~~~~~~~~~~ character.cpp:17:13: note: ‘longestGapStIndex’ was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ character.cpp: In member function ‘void character::checkForTriangleInequality(int, int)’: character.cpp:6:70: warning: ‘longestGapStIndex’ may be used uninitialized [-Wmaybe-uninitialized] 6 | if(_stepmatrix[st1][st2] > _stepmatrix[st1][longestGapStIndex]+_stepmatrix[st2][longestGapStIndex]){ | ^ character.cpp:17:13: note: ‘longestGapStIndex’ was declared here 17 | int longestGapStIndex; | ^~~~~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gaps.o gaps.cpp ar rv libindelCoder.a indelCoder.o indelCoderOptions.o indelCoderProject.o indelCoderUtils.o character.o gaps.o ar: creating libindelCoder.a a - indelCoder.o a - indelCoderOptions.o a - indelCoderProject.o a - indelCoderUtils.o a - character.o a - gaps.o ranlib libindelCoder.a powerpc64le-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder make[3]: Leaving directory '/<>/programs/indelCoder' make[2]: Leaving directory '/<>/programs' make[1]: Leaving directory '/<>' dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck" create-stamp debian/debhelper-build-stamp dh_prep -a dh_auto_install --destdir=debian/fastml/ -a make -j1 install DESTDIR=/<>/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/<>' cd libs;make all make[2]: Entering directory '/<>/libs' cd phylogeny && make all make[3]: Entering directory '/<>/libs/phylogeny' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/<>/libs/phylogeny' make[2]: Leaving directory '/<>/libs' cd programs;make install make[2]: Entering directory '/<>/programs' cd fastml && make install make[3]: Entering directory '/<>/programs/fastml' mkdir -p ../../bin cp fastml ../../bin/fastml make[3]: Leaving directory '/<>/programs/fastml' cd gainLoss && make install make[3]: Entering directory '/<>/programs/gainLoss' mkdir -p ../../bin cp gainLoss ../../bin/gainLoss make[3]: Leaving directory '/<>/programs/gainLoss' cd indelCoder && make install make[3]: Entering directory '/<>/programs/indelCoder' mkdir -p ../../bin cp indelCoder ../../bin/indelCoder make[3]: Leaving directory '/<>/programs/indelCoder' make[2]: Leaving directory '/<>/programs' make[1]: Leaving directory '/<>' dh_install -a dh_installdocs -a dh_installchangelogs -a dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'fastml' in '../fastml_3.11-4_ppc64el.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-4_ppc64el.deb'. dpkg-genbuildinfo --build=any -O../fastml_3.11-4_ppc64el.buildinfo dpkg-genchanges --build=any -O../fastml_3.11-4_ppc64el.changes dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) -------------------------------------------------------------------------------- Build finished at 2024-01-28T19:11:36Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ fastml_3.11-4_ppc64el.changes: ------------------------------ Format: 1.8 Date: Wed, 24 Jan 2024 17:23:21 +0100 Source: fastml Binary: fastml fastml-dbgsym Built-For-Profiles: cross nocheck Architecture: ppc64el Version: 3.11-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: fastml - maximum likelihood ancestral amino-acid sequence reconstruction Closes: 1044832 Changes: fastml (3.11-4) unstable; urgency=medium . * Fix clean target Closes: #1044832 * Standards-Version: 4.6.2 (routine-update) * d/watch: Upstream download vanished Checksums-Sha1: d26636c3dce1f0ad68c11d58d99f80866c9efb25 16900020 fastml-dbgsym_3.11-4_ppc64el.deb 944e955c1d3809211e4d13837ab07211753bbdbc 5694 fastml_3.11-4_ppc64el.buildinfo 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fastml-dbgsym_3.11-4_ppc64el.deb 7da5dedc4262e83557181ee5d0f07c2c 901348 fastml_3.11-4_ppc64el.deb Checksums-Sha1: d26636c3dce1f0ad68c11d58d99f80866c9efb25 16900020 fastml-dbgsym_3.11-4_ppc64el.deb 1ba094562f2f2beb5bbaf18a213de78099b3df48 901348 fastml_3.11-4_ppc64el.deb Checksums-Sha256: 51f50440742140eaf04bf100cdd53de1b63be51098d349ee31328f9a44b19e37 16900020 fastml-dbgsym_3.11-4_ppc64el.deb 9e872e575fae33937697e7c9922627a833b462ffc8ecc2b8a95aaaefe6f73b5f 901348 fastml_3.11-4_ppc64el.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Sun, 28 Jan 2024 19:11:36 +0000 Build-Path: /<> Build-Tainted-By: merged-usr-via-aliased-dirs Installed-Build-Depends: autoconf (= 2.71-3), automake (= 1:1.16.5-1.3), autopoint (= 0.21-14), autotools-dev (= 20220109.1), base-files (= 13), base-passwd (= 3.6.3), bash (= 5.2.21-2), binutils (= 2.41.90.20240122-1), binutils-common (= 2.41.90.20240122-1), binutils-x86-64-linux-gnu (= 2.41.90.20240122-1), bsdextrautils (= 2.39.3-6), bsdutils (= 1:2.39.3-6), build-essential (= 12.10), bzip2 (= 1.0.8-5+b2), coreutils (= 9.4-3+b1), cpp (= 4:13.2.0-4), cpp-11 (= 11.4.0-7), cpp-13 (= 13.2.0-12), cpp-13-x86-64-linux-gnu (= 13.2.0-12), cpp-x86-64-linux-gnu (= 4:13.2.0-4), dash (= 0.5.12-6), debconf (= 1.5.85), debhelper (= 13.13), debianutils (= 5.16), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.4), dpkg-dev (= 1.22.4), dwz (= 0.15-1), file (= 1:5.45-2+b1), findutils (= 4.9.0-5), g++ (= 4:13.2.0-4), g++-13 (= 13.2.0-12), g++-13-x86-64-linux-gnu (= 13.2.0-12), g++-x86-64-linux-gnu (= 4:13.2.0-4), gcc (= 4:13.2.0-4), gcc-11 (= 11.4.0-7), gcc-11-base (= 11.4.0-7), gcc-13 (= 13.2.0-12), gcc-13-base (= 13.2.0-12), gcc-13-x86-64-linux-gnu (= 13.2.0-12), gcc-14-base (= 14-20240127-1), gcc-x86-64-linux-gnu (= 4:13.2.0-4), gettext (= 0.21-14), gettext-base (= 0.21-14), grep (= 3.11-4), groff-base (= 1.23.0-3), gzip (= 1.12-1), hostname (= 3.23+nmu2), init-system-helpers (= 1.66), 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libgdbm-compat4 (= 1.23-5), libgdbm6 (= 1.23-5), libgmp10 (= 2:6.3.0+dfsg-2), libgomp1 (= 14-20240127-1), libgpg-error0 (= 1.47-3), libgprofng0 (= 2.41.90.20240122-1), libgssapi-krb5-2 (= 1.20.1-5), libhwasan0 (= 14-20240127-1), libicu72 (= 72.1-4), libisl23 (= 0.26-3+b2), libitm1 (= 14-20240127-1), libjansson4 (= 2.14-2+b2), libk5crypto3 (= 1.20.1-5), libkeyutils1 (= 1.6.3-2+b2), libkrb5-3 (= 1.20.1-5), libkrb5support0 (= 1.20.1-5), liblsan0 (= 14-20240127-1), liblz4-1 (= 1.9.4-1+b2), liblzma5 (= 5.4.5-0.3), libmagic-mgc (= 1:5.45-2+b1), libmagic1 (= 1:5.45-2+b1), libmd0 (= 1.1.0-2), libmount1 (= 2.39.3-6), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1), libnsl-dev (= 1.3.0-3), libnsl2 (= 1.3.0-3), libnumber-compare-perl (= 0.03-3), libpam-modules (= 1.5.2-9.1+b1), libpam-modules-bin (= 1.5.2-9.1+b1), libpam-runtime (= 1.5.2-9.1), libpam0g (= 1.5.2-9.1+b1), libpcre2-8-0 (= 10.42-4), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1+b2), libquadmath0 (= 14-20240127-1), libseccomp2 (= 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(= 4.9-2), sensible-utils (= 0.0.20), sysvinit-utils (= 3.08-6), tar (= 1.35+dfsg-3), usrmerge (= 39), util-linux (= 2.39.3-6), xz-utils (= 5.4.5-0.3), zlib1g (= 1:1.3.dfsg-3+b1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1706113401" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ fastml-dbgsym_3.11-4_ppc64el.deb -------------------------------- new Debian package, version 2.0. size 16900020 bytes: control archive=700 bytes. 450 bytes, 12 lines control 406 bytes, 4 lines md5sums Package: fastml-dbgsym Source: fastml Version: 3.11-4 Auto-Built-Package: debug-symbols Architecture: ppc64el Maintainer: Debian Med Packaging Team Installed-Size: 16927 Depends: fastml (= 3.11-4) Section: debug Priority: optional Description: debug symbols for fastml Build-Ids: 1e2e87e1084a35a873a118b5405b0e5f6b05907f d5e9593a6464720b39a4136a047c5313caa320cb d946045d06c7e2ccf57df87e293ca1fea285fd01 drwxr-xr-x root/root 0 2024-01-24 16:23 ./ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/.build-id/1e/ -rw-r--r-- root/root 8779528 2024-01-24 16:23 ./usr/lib/debug/.build-id/1e/2e87e1084a35a873a118b5405b0e5f6b05907f.debug drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/.build-id/d5/ -rw-r--r-- root/root 1257480 2024-01-24 16:23 ./usr/lib/debug/.build-id/d5/e9593a6464720b39a4136a047c5313caa320cb.debug drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/.build-id/d9/ -rw-r--r-- root/root 6066944 2024-01-24 16:23 ./usr/lib/debug/.build-id/d9/46045d06c7e2ccf57df87e293ca1fea285fd01.debug drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/.dwz/powerpc64le-linux-gnu/ -rw-r--r-- root/root 1212624 2024-01-24 16:23 ./usr/lib/debug/.dwz/powerpc64le-linux-gnu/fastml.debug drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/share/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/share/doc/ lrwxrwxrwx root/root 0 2024-01-24 16:23 ./usr/share/doc/fastml-dbgsym -> fastml fastml_3.11-4_ppc64el.deb ------------------------- new Debian package, version 2.0. size 901348 bytes: control archive=1244 bytes. 1438 bytes, 26 lines control 494 bytes, 8 lines md5sums Package: fastml Version: 3.11-4 Architecture: ppc64el Maintainer: Debian Med Packaging Team Installed-Size: 4058 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.4.4), libstdc++6 (>= 13.1) Section: science Priority: optional Homepage: http://fastml.tau.ac.il/ Description: maximum likelihood ancestral amino-acid sequence reconstruction FastML is a bioinformatics tool for the reconstruction of ancestral sequences based on the phylogenetic relations between homologous sequences. FastML runs several algorithms that reconstruct the ancestral sequences with emphasis on an accurate reconstruction of both indels and characters. For character reconstruction the previously described FastML algorithms are used to efficiently infer the most likely ancestral sequences for each internal node of the tree. Both joint and the marginal reconstructions are provided. For indels reconstruction the sequences are first coded according to the indel events detected within the multiple sequence alignment (MSA) and then a state-of-the-art likelihood model is used to reconstruct ancestral indels states. The results are the most probable sequences, together with posterior probabilities for each character and indel at each sequence position for each internal node of the tree. FastML is generic and is applicable for any type of molecular sequences (nucleotide, protein, or codon sequences). drwxr-xr-x root/root 0 2024-01-24 16:23 ./ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/bin/ -rwxr-xr-x root/root 1444192 2024-01-24 16:23 ./usr/bin/fastml -rwxr-xr-x root/root 2296160 2024-01-24 16:23 ./usr/bin/gainLoss -rwxr-xr-x root/root 395616 2024-01-24 16:23 ./usr/bin/indelCoder drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/share/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/share/doc/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/share/doc/fastml/ -rw-r--r-- root/root 551 2024-01-24 16:23 ./usr/share/doc/fastml/changelog.Debian.gz -rw-r--r-- root/root 2937 2024-01-24 16:23 ./usr/share/doc/fastml/copyright drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/share/man/ drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/share/man/man1/ -rw-r--r-- root/root 1491 2024-01-24 16:23 ./usr/share/man/man1/fastml.1.gz -rw-r--r-- root/root 480 2024-01-24 16:23 ./usr/share/man/man1/gainLoss.1.gz -rw-r--r-- root/root 215 2024-01-24 16:23 ./usr/share/man/man1/indelCoder.1.gz lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [615 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [1302 B] Get:5 copy:/<>/apt_archive ./ Packages [1385 B] Fetched 3302 B in 0s (0 B/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following additional packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common t1utils unzip Suggested packages: isoquery libxml-parser-perl libdata-dump-perl libcrypt-ssleay-perl libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libbusiness-isbn-perl libregexp-ipv6-perl libauthen-ntlm-perl binutils-multiarch libtext-template-perl readline-doc zip Recommended packages: gnupg libcgi-fast-perl libhtml-format-perl libio-compress-brotli-perl liblist-someutils-xs-perl libfreezethaw-perl libmath-base85-perl libsocket6-perl libpackage-stash-xs-perl libxstring-perl libdata-dump-perl libhttp-daemon-perl libmailtools-perl The following NEW packages will be installed: ca-certificates diffstat gpg gpgconf iso-codes libaliased-perl libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libberkeleydb-perl libcapture-tiny-perl libcgi-pm-perl libclass-data-inheritable-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libconfig-tiny-perl libconst-fast-perl libcpanel-json-xs-perl libdata-dpath-perl libdata-messagepack-perl libdata-optlist-perl libdata-validate-domain-perl libdata-validate-ip-perl libdata-validate-uri-perl libdevel-callchecker-perl libdevel-size-perl libdevel-stacktrace-perl libdynaloader-functions-perl libemail-address-xs-perl libencode-locale-perl libexception-class-perl libfile-basedir-perl libfile-listing-perl libfont-ttf-perl libhtml-form-perl libhtml-html5-entities-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tokeparser-simple-perl libhtml-tree-perl libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libimport-into-perl libio-html-perl libio-interactive-perl libio-socket-ssl-perl libipc-run3-perl libipc-system-simple-perl libiterator-perl libiterator-util-perl libjson-maybexs-perl liblist-compare-perl liblist-someutils-perl liblist-utilsby-perl liblwp-mediatypes-perl liblwp-protocol-https-perl liblz1 liblzo2-2 libmarkdown2 libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libmouse-perl libnamespace-clean-perl libnet-domain-tld-perl libnet-http-perl libnet-ipv6addr-perl libnet-netmask-perl libnet-ssleay-perl libnetaddr-ip-perl libpackage-stash-perl libparams-classify-perl libparams-util-perl libpath-tiny-perl libperlio-gzip-perl libperlio-utf8-strict-perl libproc-processtable-perl libreadline8 libregexp-wildcards-perl librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsort-versions-perl libsqlite3-0 libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-quote-perl libsyntax-keyword-try-perl libterm-readkey-perl libtext-levenshteinxs-perl libtext-markdown-discount-perl libtext-xslate-perl libtime-duration-perl libtime-moment-perl libtimedate-perl libtry-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libwww-mechanize-perl libwww-perl libwww-robotrules-perl libxs-parse-keyword-perl libyaml-0-2 libyaml-libyaml-perl lintian lzop netbase openssl patchutils perl-openssl-defaults plzip readline-common sbuild-build-depends-lintian-dummy:ppc64el t1utils unzip 0 upgraded, 126 newly installed, 0 to remove and 0 not upgraded. Need to get 13.8 MB of archives. After this operation, 51.9 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [852 B] Get:2 http://localhost:3142/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:3 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:4 http://localhost:3142/debian sid/main amd64 openssl amd64 3.1.4-2 [1426 kB] Get:5 http://localhost:3142/debian sid/main amd64 ca-certificates all 20230311 [153 kB] Get:6 http://localhost:3142/debian sid/main amd64 diffstat amd64 1.65-1 [33.3 kB] Get:7 http://localhost:3142/debian sid/main amd64 libassuan0 amd64 2.5.6-1 [49.9 kB] Get:8 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:9 http://localhost:3142/debian sid/main amd64 gpgconf amd64 2.2.40-1.1+b1 [565 kB] Get:10 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.45.0-1 [894 kB] Get:11 http://localhost:3142/debian sid/main amd64 gpg amd64 2.2.40-1.1+b1 [950 kB] Get:12 http://localhost:3142/debian sid/main amd64 iso-codes all 4.16.0-1 [2936 kB] Get:13 http://localhost:3142/debian sid/main amd64 libaliased-perl all 0.34-3 [13.5 kB] Get:14 http://localhost:3142/debian sid/main amd64 libapt-pkg-perl amd64 0.1.40+b3 [66.9 kB] Get:15 http://localhost:3142/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB] Get:16 http://localhost:3142/debian sid/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:17 http://localhost:3142/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB] Get:18 http://localhost:3142/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB] Get:19 http://localhost:3142/debian sid/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:20 http://localhost:3142/debian sid/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:21 http://localhost:3142/debian sid/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:22 http://localhost:3142/debian sid/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:23 http://localhost:3142/debian sid/main amd64 libvariable-magic-perl amd64 0.63-1+b2 [43.9 kB] Get:24 http://localhost:3142/debian sid/main amd64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:25 http://localhost:3142/debian sid/main amd64 libberkeleydb-perl amd64 0.64-2+b2 [121 kB] Get:26 http://localhost:3142/debian sid/main amd64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:27 http://localhost:3142/debian sid/main amd64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:28 http://localhost:3142/debian sid/main amd64 liburi-perl all 5.21-1 [95.6 kB] Get:29 http://localhost:3142/debian sid/main amd64 libhtml-parser-perl amd64 3.81-1+b1 [99.0 kB] Get:30 http://localhost:3142/debian sid/main amd64 libcgi-pm-perl all 4.61-1 [217 kB] Get:31 http://localhost:3142/debian sid/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:32 http://localhost:3142/debian sid/main amd64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:33 http://localhost:3142/debian sid/main amd64 libclass-xsaccessor-perl amd64 1.19-4+b2 [36.3 kB] Get:34 http://localhost:3142/debian sid/main amd64 libclone-perl amd64 0.46-1+b1 [13.8 kB] Get:35 http://localhost:3142/debian sid/main amd64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:36 http://localhost:3142/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b2 [24.4 kB] Get:37 http://localhost:3142/debian sid/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:38 http://localhost:3142/debian sid/main amd64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:39 http://localhost:3142/debian sid/main amd64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:40 http://localhost:3142/debian sid/main amd64 libconst-fast-perl all 0.014-2 [8792 B] Get:41 http://localhost:3142/debian sid/main amd64 libcpanel-json-xs-perl amd64 4.37-1+b1 [128 kB] Get:42 http://localhost:3142/debian sid/main amd64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:43 http://localhost:3142/debian sid/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:44 http://localhost:3142/debian sid/main amd64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:45 http://localhost:3142/debian sid/main amd64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:46 http://localhost:3142/debian sid/main amd64 libdata-dpath-perl all 0.59-1 [43.6 kB] Get:47 http://localhost:3142/debian sid/main amd64 libdata-messagepack-perl amd64 1.02-1+b2 [32.6 kB] Get:48 http://localhost:3142/debian sid/main amd64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:49 http://localhost:3142/debian sid/main amd64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:50 http://localhost:3142/debian sid/main amd64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:51 http://localhost:3142/debian sid/main amd64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:52 http://localhost:3142/debian sid/main amd64 libnetaddr-ip-perl amd64 4.079+dfsg-2+b2 [98.1 kB] Get:53 http://localhost:3142/debian sid/main amd64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:54 http://localhost:3142/debian sid/main amd64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:55 http://localhost:3142/debian sid/main amd64 libdevel-size-perl amd64 0.83-2+b2 [24.3 kB] Get:56 http://localhost:3142/debian sid/main amd64 libemail-address-xs-perl amd64 1.05-1+b2 [29.3 kB] Get:57 http://localhost:3142/debian sid/main amd64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:58 http://localhost:3142/debian sid/main amd64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:59 http://localhost:3142/debian sid/main amd64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:60 http://localhost:3142/debian sid/main amd64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:61 http://localhost:3142/debian sid/main amd64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:62 http://localhost:3142/debian sid/main amd64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:63 http://localhost:3142/debian sid/main amd64 libfont-ttf-perl all 1.06-2 [318 kB] Get:64 http://localhost:3142/debian sid/main amd64 libio-html-perl all 1.004-3 [16.2 kB] Get:65 http://localhost:3142/debian sid/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:66 http://localhost:3142/debian sid/main amd64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:67 http://localhost:3142/debian sid/main amd64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:68 http://localhost:3142/debian sid/main amd64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:69 http://localhost:3142/debian sid/main amd64 libhtml-tree-perl all 5.07-3 [211 kB] Get:70 http://localhost:3142/debian sid/main amd64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:71 http://localhost:3142/debian sid/main amd64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:72 http://localhost:3142/debian sid/main amd64 perl-openssl-defaults amd64 7+b1 [7924 B] Get:73 http://localhost:3142/debian sid/main amd64 libnet-ssleay-perl amd64 1.94-1 [338 kB] Get:74 http://localhost:3142/debian sid/main amd64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get:75 http://localhost:3142/debian sid/main amd64 libnet-http-perl all 6.23-1 [23.9 kB] Get:76 http://localhost:3142/debian sid/main amd64 liblwp-protocol-https-perl all 6.12-1 [10.5 kB] Get:77 http://localhost:3142/debian sid/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:78 http://localhost:3142/debian sid/main amd64 libwww-perl all 6.76-1 [183 kB] Get:79 http://localhost:3142/debian sid/main amd64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:80 http://localhost:3142/debian sid/main amd64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:81 http://localhost:3142/debian sid/main amd64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:82 http://localhost:3142/debian sid/main amd64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:83 http://localhost:3142/debian sid/main amd64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get:84 http://localhost:3142/debian sid/main amd64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:85 http://localhost:3142/debian sid/main amd64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:86 http://localhost:3142/debian sid/main amd64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:87 http://localhost:3142/debian sid/main amd64 liblz1 amd64 1.14-1 [38.5 kB] Get:88 http://localhost:3142/debian sid/main amd64 liblzo2-2 amd64 2.10-2 [56.9 kB] Get:89 http://localhost:3142/debian sid/main amd64 libmarkdown2 amd64 2.2.7-2+b1 [35.6 kB] Get:90 http://localhost:3142/debian sid/main amd64 libmldbm-perl all 2.05-4 [16.8 kB] Get:91 http://localhost:3142/debian sid/main amd64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:92 http://localhost:3142/debian sid/main amd64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:93 http://localhost:3142/debian sid/main amd64 libmoo-perl all 2.005005-1 [58.0 kB] Get:94 http://localhost:3142/debian sid/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:95 http://localhost:3142/debian sid/main amd64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:96 http://localhost:3142/debian sid/main amd64 libmouse-perl amd64 2.5.10-1+b4 [143 kB] Get:97 http://localhost:3142/debian sid/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:98 http://localhost:3142/debian sid/main amd64 libsub-identify-perl amd64 0.14-3+b1 [11.2 kB] Get:99 http://localhost:3142/debian sid/main amd64 libsub-name-perl amd64 0.27-1+b1 [12.5 kB] Get:100 http://localhost:3142/debian sid/main amd64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:101 http://localhost:3142/debian sid/main amd64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:102 http://localhost:3142/debian sid/main amd64 libperlio-gzip-perl amd64 0.20-1+b2 [17.5 kB] Get:103 http://localhost:3142/debian sid/main amd64 libperlio-utf8-strict-perl amd64 0.010-1+b1 [11.4 kB] Get:104 http://localhost:3142/debian sid/main amd64 libproc-processtable-perl amd64 0.636-1+b1 [42.2 kB] Get:105 http://localhost:3142/debian sid/main amd64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:106 http://localhost:3142/debian sid/main amd64 libsereal-decoder-perl amd64 5.004+ds-1+b1 [99.2 kB] Get:107 http://localhost:3142/debian sid/main amd64 libsereal-encoder-perl amd64 5.004+ds-1+b1 [102 kB] Get:108 http://localhost:3142/debian sid/main amd64 libsort-versions-perl all 1.62-3 [8928 B] Get:109 http://localhost:3142/debian sid/main amd64 libxs-parse-keyword-perl amd64 0.39-1+b1 [57.5 kB] Get:110 http://localhost:3142/debian sid/main amd64 libsyntax-keyword-try-perl amd64 0.29-1+b1 [27.1 kB] Get:111 http://localhost:3142/debian sid/main amd64 libterm-readkey-perl amd64 2.38-2+b2 [24.7 kB] Get:112 http://localhost:3142/debian sid/main amd64 libtext-levenshteinxs-perl amd64 0.03-5+b2 [8704 B] Get:113 http://localhost:3142/debian sid/main amd64 libtext-markdown-discount-perl amd64 0.16-1+b1 [13.0 kB] Get:114 http://localhost:3142/debian sid/main amd64 libtext-xslate-perl amd64 3.5.9-1+b3 [174 kB] Get:115 http://localhost:3142/debian sid/main amd64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:116 http://localhost:3142/debian sid/main amd64 libtime-moment-perl amd64 0.44-2+b2 [72.7 kB] Get:117 http://localhost:3142/debian sid/main amd64 libunicode-utf8-perl amd64 0.62-2+b1 [20.3 kB] Get:118 http://localhost:3142/debian sid/main amd64 libwww-mechanize-perl all 2.17-1 [116 kB] Get:119 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:120 http://localhost:3142/debian sid/main amd64 libyaml-libyaml-perl amd64 0.86+ds-1+b1 [34.2 kB] Get:121 http://localhost:3142/debian sid/main amd64 plzip amd64 1.11-1 [63.9 kB] Get:122 http://localhost:3142/debian sid/main amd64 lzop amd64 1.04-2 [84.2 kB] Get:123 http://localhost:3142/debian sid/main amd64 patchutils amd64 0.4.2-1 [77.5 kB] Get:124 http://localhost:3142/debian sid/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:125 http://localhost:3142/debian sid/main amd64 unzip amd64 6.0-28 [166 kB] Get:126 http://localhost:3142/debian sid/main amd64 lintian all 2.116.3 [1130 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 13.8 MB in 0s (104 MB/s) Selecting previously unselected package netbase. (Reading database ... 22323 files and directories currently installed.) Preparing to unpack .../000-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package readline-common. Preparing to unpack .../001-readline-common_8.2-3_all.deb ... Unpacking readline-common (8.2-3) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.1.4-2_amd64.deb ... Unpacking openssl (3.1.4-2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.65-1_amd64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../005-libassuan0_2.5.6-1_amd64.deb ... Unpacking libassuan0:amd64 (2.5.6-1) ... Selecting previously unselected package libreadline8:amd64. 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Unpacking libapt-pkg-perl (0.1.40+b3) ... Selecting previously unselected package libb-hooks-op-check-perl:amd64. Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-2+b2_amd64.deb ... Unpacking libb-hooks-op-check-perl:amd64 (0.22-2+b2) ... Selecting previously unselected package libdynaloader-functions-perl. Preparing to unpack .../014-libdynaloader-functions-perl_0.003-3_all.deb ... Unpacking libdynaloader-functions-perl (0.003-3) ... Selecting previously unselected package libdevel-callchecker-perl:amd64. Preparing to unpack .../015-libdevel-callchecker-perl_0.008-2+b1_amd64.deb ... Unpacking libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Selecting previously unselected package libparams-classify-perl:amd64. Preparing to unpack .../016-libparams-classify-perl_0.015-2+b2_amd64.deb ... Unpacking libparams-classify-perl:amd64 (0.015-2+b2) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../017-libmodule-runtime-perl_0.016-2_all.deb ... 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Setting up liblz1:amd64 (1.14-1) ... Setting up libberkeleydb-perl:amd64 (0.64-2+b2) ... Setting up plzip (1.11-1) ... update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip (lzip) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-compressor (lzip-compressor) in auto mode update-alternatives: using /usr/bin/lzip.plzip to provide /usr/bin/lzip-decompressor (lzip-decompressor) in auto mode Setting up libunicode-utf8-perl (0.62-2+b1) ... Setting up libmouse-perl (2.5.10-1+b4) ... Setting up libdata-messagepack-perl (1.02-1+b2) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libclass-method-modifiers-perl (2.15-1) ... Setting up liblist-compare-perl (0.55-2) ... Setting up libclone-perl:amd64 (0.46-1+b1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3+b1) ... Setting up libcpanel-json-xs-perl:amd64 (4.37-1+b1) ... Setting up libhtml-tagset-perl (3.20-6) ... Setting up libdevel-size-perl (0.83-2+b2) ... Setting up unzip (6.0-28) ... Setting up libsqlite3-0:amd64 (3.45.0-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.86+ds-1+b1) ... Setting up libio-interactive-perl (1.025-1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:amd64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:amd64 (2.10-2) ... Setting up libtime-moment-perl (0.44-2+b2) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:amd64 (2.5.6-1) ... Setting up libconfig-tiny-perl (2.30-1) ... Setting up libsereal-encoder-perl (5.004+ds-1+b1) ... Setting up liblist-utilsby-perl (0.12-2) ... Setting up libnet-netmask-perl (2.0002-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up patchutils (0.4.2-1) ... Setting up libjson-maybexs-perl (1.004005-1) ... Setting up libnetaddr-ip-perl (4.079+dfsg-2+b2) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libxs-parse-keyword-perl (0.39-1+b1) ... Setting up libipc-system-simple-perl (1.30-2) ... Setting up libnet-domain-tld-perl (1.75-3) ... Setting up libperlio-utf8-strict-perl (0.010-1+b1) ... Setting up t1utils (1.41-4) ... Setting up diffstat (1.65-1) ... Setting up libvariable-magic-perl (0.63-1+b2) ... Setting up libio-html-perl (1.004-3) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b2) ... Setting up libparams-util-perl (1.102-2+b2) ... Setting up libtime-duration-perl (1.21-2) ... Setting up libtext-xslate-perl:amd64 (3.5.9-1+b3) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libcapture-tiny-perl (0.48-2) ... Setting up libtimedate-perl (2.3300-2) ... Setting up libsub-name-perl:amd64 (0.27-1+b1) ... Setting up libsyntax-keyword-try-perl (0.29-1+b1) ... Setting up libdata-validate-domain-perl (0.10-1.1) ... Setting up libproc-processtable-perl:amd64 (0.636-1+b1) ... Setting up libpath-tiny-perl (0.144-1) ... Setting up lzop (1.04-2) ... Setting up librole-tiny-perl (2.002004-1) ... Setting up libipc-run3-perl (0.049-1) ... Setting up libregexp-wildcards-perl (1.05-3) ... Setting up libaliased-perl (0.34-3) ... Setting up netbase (6.4) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006008-1) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libclass-xsaccessor-perl (1.19-4+b2) ... Setting up libsort-versions-perl (1.62-3) ... Setting up libterm-readkey-perl (2.38-2+b2) ... Setting up libfont-ttf-perl (1.06-2) ... Setting up openssl (3.1.4-2) ... Setting up libtext-levenshteinxs-perl (0.03-5+b2) ... Setting up libperlio-gzip-perl (0.20-1+b2) ... Setting up readline-common (8.2-3) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1+b1) ... Setting up libmarkdown2:amd64 (2.2.7-2+b1) ... Setting up liburi-perl (5.21-1) ... Setting up iso-codes (4.16.0-1) ... Setting up libnet-ipv6addr-perl (1.02-1) ... Setting up libdata-validate-ip-perl (0.31-1) ... Setting up libemail-address-xs-perl (1.05-1+b2) ... Setting up libnet-ssleay-perl:amd64 (1.94-1) ... Setting up libhttp-date-perl (6.06-1) ... Setting up libfile-basedir-perl (0.09-2) ... Setting up libfile-listing-perl (6.16-1) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up libnet-http-perl (6.23-1) ... Setting up libtext-markdown-discount-perl (0.16-1+b1) ... Setting up libexception-class-perl (1.45-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libdata-validate-uri-perl (0.07-2) ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl:amd64 (3.81-1+b1) ... Setting up gpgconf (2.2.40-1.1+b1) ... Setting up libio-socket-ssl-perl (2.085-1) ... Setting up gpg (2.2.40-1.1+b1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libhttp-message-perl (6.45-1) ... Setting up libhtml-form-perl (6.11-1) ... Setting up libiterator-perl (0.03+ds1-2) ... Setting up libhttp-negotiate-perl (6.01-2) ... Setting up libiterator-util-perl (0.02+ds1-2) ... Setting up libhttp-cookies-perl (6.11-1) ... Setting up libhtml-tree-perl (5.07-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b2) ... Setting up libcgi-pm-perl (4.61-1) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libconst-fast-perl (0.014-2) ... Setting up libdata-dpath-perl (0.59-1) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libimport-into-perl (1.002005-2) ... Setting up libmoo-perl (2.005005-1) ... Setting up liblist-someutils-perl (0.59-1) ... Setting up libmoox-aliases-perl (0.001006-2) ... Setting up libb-hooks-endofscope-perl (0.26-1) ... Setting up libnamespace-clean-perl (0.27-2) ... Setting up libwww-perl (6.76-1) ... Setting up libhtml-tokeparser-simple-perl (3.16-4) ... Setting up libwww-mechanize-perl (2.17-1) ... Setting up liblwp-protocol-https-perl (6.12-1) ... Setting up lintian (2.116.3) ... Setting up sbuild-build-depends-lintian-dummy:ppc64el (0.invalid.0) ... Processing triggers for libc-bin (2.37-14) ... Processing triggers for man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Running lintian... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 487224 Build-Time: 318 Distribution: unstable Foreign Architectures: ppc64el Host Architecture: ppc64el Install-Time: 13 Job: fastml_3.11-4 Lintian: pass Machine Architecture: amd64 Package: fastml Package-Time: 342 Source-Version: 3.11-4 Space: 487224 Status: successful Version: 3.11-4 -------------------------------------------------------------------------------- Finished at 2024-01-28T19:11:36Z Build needed 00:05:42, 487224k disk space