sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org +==============================================================================+ | fastml 3.11-4 (i386) Fri, 01 Mar 2024 19:54:27 +0000 | +==============================================================================+ Package: fastml Version: 3.11-4 Source Version: 3.11-4 Distribution: unstable Machine Architecture: arm64 Host Architecture: i386 Build Architecture: arm64 Build Profiles: cross nocheck Build Type: any Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.3cBnEdm1fE... I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-TxSayE/resolver-o0STAr' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://mirror.einval.org/debian unstable InRelease [198 kB] Get:2 http://mirror.einval.org/debian unstable/main Sources [10.6 MB] Get:3 http://mirror.einval.org/debian unstable/main i386 Packages [9753 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 Packages [9819 kB] Fetched 30.4 MB in 8s (3922 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libcom-err2 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnsl-dev libnsl2 libtirpc-common libtirpc-dev libtirpc3t64 Use 'apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libgnutls30 libtirpc3 libuuid1 The following NEW packages will be installed: libapt-pkg6.0t64 libgnutls30t64 libtirpc3t64 libuuid1t64 The following packages have been kept back: util-linux The following packages will be upgraded: apt bsdutils cpp-13 cpp-13-aarch64-linux-gnu dpkg dpkg-dev g++-13 g++-13-aarch64-linux-gnu gcc-13 gcc-13-aarch64-linux-gnu gcc-13-base gcc-14-base libasan8 libatomic1 libaudit-common libaudit1 libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcc1-0 libdpkg-perl libgcc-13-dev libgcc-s1 libgomp1 libhwasan0 libitm1 liblsan0 liblzma5 libmount1 libpam-modules libpam-modules-bin libpam-runtime libpam0g libsmartcols1 libstdc++-13-dev libstdc++6 libsystemd0 libtirpc-common libtirpc-dev libtsan2 libubsan1 libudev1 sysvinit-utils xz-utils zlib1g 47 upgraded, 4 newly installed, 4 to remove and 1 not upgraded. Need to get 63.9 MB of archives. After this operation, 233 kB disk space will be freed. Get:1 http://mirror.einval.org/debian unstable/main arm64 bsdutils arm64 1:2.39.3-6.1 [97.4 kB] Get:2 http://mirror.einval.org/debian unstable/main arm64 libc6-dev arm64 2.37-15.1 [1433 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 libc-dev-bin arm64 2.37-15.1 [46.2 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 libasan8 arm64 14-20240221-2.1 [2566 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 libubsan1 arm64 14-20240221-2.1 [1035 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 cpp-13 arm64 13.2.0-16.1 [1280 B] Get:7 http://mirror.einval.org/debian unstable/main arm64 cpp-13-aarch64-linux-gnu arm64 13.2.0-16.1 [8865 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 g++-13 arm64 13.2.0-16.1 [14.7 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 gcc-13 arm64 13.2.0-16.1 [466 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 gcc-13-aarch64-linux-gnu arm64 13.2.0-16.1 [16.9 MB] Get:11 http://mirror.einval.org/debian unstable/main arm64 g++-13-aarch64-linux-gnu arm64 13.2.0-16.1 [9738 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 libstdc++-13-dev arm64 13.2.0-16.1 [2142 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 gcc-13-base arm64 13.2.0-16.1 [43.3 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libgcc-13-dev arm64 13.2.0-16.1 [2236 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libtsan2 arm64 14-20240221-2.1 [2377 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 liblsan0 arm64 14-20240221-2.1 [1156 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libitm1 arm64 14-20240221-2.1 [23.6 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libhwasan0 arm64 14-20240221-2.1 [1434 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libgomp1 arm64 14-20240221-2.1 [122 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 gcc-14-base arm64 14-20240221-2.1 [42.8 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1 arm64 14-20240221-2.1 [43.6 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libcc1-0 arm64 14-20240221-2.1 [37.6 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libatomic1 arm64 14-20240221-2.1 [9960 B] Get:24 http://mirror.einval.org/debian unstable/main arm64 libstdc++6 arm64 14-20240221-2.1 [635 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 zlib1g arm64 1:1.3.dfsg-3.1 [83.8 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libc6 arm64 2.37-15.1 [2321 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 liblzma5 arm64 5.6.0-0.2 [216 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libsystemd0 arm64 255.4-1 [337 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libudev1 arm64 255.4-1 [118 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.3-1.1 [1333 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg6.0t64 arm64 2.7.13+b1 [877 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 apt arm64 2.7.13+b1 [1293 kB] Get:33 http://mirror.einval.org/debian unstable/main arm64 dpkg arm64 1.22.5 [1494 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libc-bin arm64 2.37-15.1 [526 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 sysvinit-utils arm64 3.08-7 [32.1 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libtirpc-common all 1.3.4+ds-1.1 [10.8 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libtirpc-dev arm64 1.3.4+ds-1.1 [192 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libtirpc3t64 arm64 1.3.4+ds-1.1 [78.4 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libuuid1t64 arm64 2.39.3-6.1 [29.7 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libaudit1 arm64 1:3.1.2-2.1 [48.0 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libpam0g arm64 1.5.3-6 [66.3 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libpam-modules-bin arm64 1.5.3-6 [53.1 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libpam-modules arm64 1.5.3-6 [255 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libpam-runtime all 1.5.3-6 [140 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libblkid1 arm64 2.39.3-6.1 [155 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libmount1 arm64 2.39.3-6.1 [183 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libsmartcols1 arm64 2.39.3-6.1 [114 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 xz-utils arm64 5.6.0-0.2 [488 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 dpkg-dev all 1.22.5 [1303 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libdpkg-perl all 1.22.5 [632 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 63.9 MB in 1s (82.9 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12121 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.39.3-6.1_arm64.deb ... Unpacking bsdutils (1:2.39.3-6.1) over (1:2.39.3-6) ... Setting up bsdutils (1:2.39.3-6.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12121 files and directories currently installed.) Preparing to unpack .../00-libc6-dev_2.37-15.1_arm64.deb ... Unpacking libc6-dev:arm64 (2.37-15.1) over (2.37-15) ... Preparing to unpack .../01-libc-dev-bin_2.37-15.1_arm64.deb ... Unpacking libc-dev-bin (2.37-15.1) over (2.37-15) ... Preparing to unpack .../02-libasan8_14-20240221-2.1_arm64.deb ... Unpacking libasan8:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../03-libubsan1_14-20240221-2.1_arm64.deb ... Unpacking libubsan1:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../04-cpp-13_13.2.0-16.1_arm64.deb ... Unpacking cpp-13 (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../05-cpp-13-aarch64-linux-gnu_13.2.0-16.1_arm64.deb ... Unpacking cpp-13-aarch64-linux-gnu (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../06-g++-13_13.2.0-16.1_arm64.deb ... Unpacking g++-13 (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../07-gcc-13_13.2.0-16.1_arm64.deb ... Unpacking gcc-13 (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../08-gcc-13-aarch64-linux-gnu_13.2.0-16.1_arm64.deb ... Unpacking gcc-13-aarch64-linux-gnu (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../09-g++-13-aarch64-linux-gnu_13.2.0-16.1_arm64.deb ... Unpacking g++-13-aarch64-linux-gnu (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../10-libstdc++-13-dev_13.2.0-16.1_arm64.deb ... Unpacking libstdc++-13-dev:arm64 (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../11-gcc-13-base_13.2.0-16.1_arm64.deb ... Unpacking gcc-13-base:arm64 (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../12-libgcc-13-dev_13.2.0-16.1_arm64.deb ... Unpacking libgcc-13-dev:arm64 (13.2.0-16.1) over (13.2.0-13) ... Preparing to unpack .../13-libtsan2_14-20240221-2.1_arm64.deb ... Unpacking libtsan2:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../14-liblsan0_14-20240221-2.1_arm64.deb ... Unpacking liblsan0:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../15-libitm1_14-20240221-2.1_arm64.deb ... Unpacking libitm1:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../16-libhwasan0_14-20240221-2.1_arm64.deb ... Unpacking libhwasan0:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../17-libgomp1_14-20240221-2.1_arm64.deb ... Unpacking libgomp1:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../18-gcc-14-base_14-20240221-2.1_arm64.deb ... Unpacking gcc-14-base:arm64 (14-20240221-2.1) over (14-20240201-3) ... Setting up gcc-14-base:arm64 (14-20240221-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12121 files and directories currently installed.) Preparing to unpack .../libgcc-s1_14-20240221-2.1_arm64.deb ... Unpacking libgcc-s1:arm64 (14-20240221-2.1) over (14-20240201-3) ... Setting up libgcc-s1:arm64 (14-20240221-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12121 files and directories currently installed.) Preparing to unpack .../libcc1-0_14-20240221-2.1_arm64.deb ... Unpacking libcc1-0:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../libatomic1_14-20240221-2.1_arm64.deb ... Unpacking libatomic1:arm64 (14-20240221-2.1) over (14-20240201-3) ... Preparing to unpack .../libstdc++6_14-20240221-2.1_arm64.deb ... Unpacking libstdc++6:arm64 (14-20240221-2.1) over (14-20240201-3) ... Setting up libstdc++6:arm64 (14-20240221-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12121 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.3.dfsg-3.1_arm64.deb ... Unpacking zlib1g:arm64 (1:1.3.dfsg-3.1) over (1:1.3.dfsg-3+b1) ... Setting up zlib1g:arm64 (1:1.3.dfsg-3.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12120 files and directories currently installed.) Preparing to unpack .../libc6_2.37-15.1_arm64.deb ... Unpacking libc6:arm64 (2.37-15.1) over (2.37-15) ... Setting up libc6:arm64 (2.37-15.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12120 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.0-0.2_arm64.deb ... Unpacking liblzma5:arm64 (5.6.0-0.2) over (5.4.5-0.3) ... Setting up liblzma5:arm64 (5.6.0-0.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12120 files and directories currently installed.) Preparing to unpack .../libsystemd0_255.4-1_arm64.deb ... Unpacking libsystemd0:arm64 (255.4-1) over (255.3-2) ... Setting up libsystemd0:arm64 (255.4-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12120 files and directories currently installed.) Preparing to unpack .../libudev1_255.4-1_arm64.deb ... Unpacking libudev1:arm64 (255.4-1) over (255.3-2) ... Setting up libudev1:arm64 (255.4-1) ... dpkg: libgnutls30:arm64: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.8.1). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12120 files and directories currently installed.) Removing libgnutls30:arm64 (3.8.3-1) ... Selecting previously unselected package libgnutls30t64:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12092 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.3-1.1_arm64.deb ... Unpacking libgnutls30t64:arm64 (3.8.3-1.1) ... Setting up libgnutls30t64:arm64 (3.8.3-1.1) ... dpkg: libapt-pkg6.0:arm64: dependency problems, but removing anyway as you requested: apt depends on libapt-pkg6.0 (>= 2.7.12). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12121 files and directories currently installed.) Removing libapt-pkg6.0:arm64 (2.7.12) ... Selecting previously unselected package libapt-pkg6.0t64:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12072 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.13+b1_arm64.deb ... Unpacking libapt-pkg6.0t64:arm64 (2.7.13+b1) ... Setting up libapt-pkg6.0t64:arm64 (2.7.13+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12123 files and directories currently installed.) Preparing to unpack .../apt_2.7.13+b1_arm64.deb ... Unpacking apt (2.7.13+b1) over (2.7.12) ... Setting up apt (2.7.13+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12124 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.22.5_arm64.deb ... Unpacking dpkg (1.22.5) over (1.22.4) ... Setting up dpkg (1.22.5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12124 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-15.1_arm64.deb ... Unpacking libc-bin (2.37-15.1) over (2.37-15) ... Setting up libc-bin (2.37-15.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12124 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-7_arm64.deb ... Unpacking sysvinit-utils (3.08-7) over (3.08-6) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.08-7) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12124 files and directories currently installed.) Preparing to unpack .../libtirpc-common_1.3.4+ds-1.1_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.1) over (1.3.4+ds-1) ... Preparing to unpack .../libtirpc-dev_1.3.4+ds-1.1_arm64.deb ... Unpacking libtirpc-dev:arm64 (1.3.4+ds-1.1) over (1.3.4+ds-1) ... dpkg: libtirpc3:arm64: dependency problems, but removing anyway as you requested: libnsl2:arm64 depends on libtirpc3 (>= 1.0.2). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12124 files and directories currently installed.) Removing libtirpc3:arm64 (1.3.4+ds-1) ... Selecting previously unselected package libtirpc3t64:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12117 files and directories currently installed.) Preparing to unpack .../libtirpc3t64_1.3.4+ds-1.1_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3 to /lib/aarch64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/aarch64-linux-gnu/libtirpc.so.3.0.0 to /lib/aarch64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:arm64 (1.3.4+ds-1.1) ... dpkg: libuuid1:arm64: dependency problems, but removing anyway as you requested: util-linux depends on libuuid1 (>= 2.16). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12129 files and directories currently installed.) Removing libuuid1:arm64 (2.39.3-6) ... Selecting previously unselected package libuuid1t64:arm64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12123 files and directories currently installed.) Preparing to unpack .../libuuid1t64_2.39.3-6.1_arm64.deb ... Unpacking libuuid1t64:arm64 (2.39.3-6.1) ... Setting up libuuid1t64:arm64 (2.39.3-6.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12130 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2.1_all.deb ... Unpacking libaudit-common (1:3.1.2-2.1) over (1:3.1.2-2) ... Setting up libaudit-common (1:3.1.2-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12130 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-2.1_arm64.deb ... Unpacking libaudit1:arm64 (1:3.1.2-2.1) over (1:3.1.2-2) ... Setting up libaudit1:arm64 (1:3.1.2-2.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12130 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-6_arm64.deb ... Unpacking libpam0g:arm64 (1.5.3-6) over (1.5.2-9.1+b1) ... Setting up libpam0g:arm64 (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12129 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-6_arm64.deb ... Unpacking libpam-modules-bin (1.5.3-6) over (1.5.2-9.1+b1) ... Setting up libpam-modules-bin (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12128 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-6_arm64.deb ... Unpacking libpam-modules:arm64 (1.5.3-6) over (1.5.2-9.1+b1) ... dpkg: warning: unable to delete old directory '/lib/aarch64-linux-gnu/security': Directory not empty Setting up libpam-modules:arm64 (1.5.3-6) ... Installing new version of config file /etc/security/namespace.init ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12125 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.5.3-6_all.deb ... Unpacking libpam-runtime (1.5.3-6) over (1.5.2-9.1) ... Setting up libpam-runtime (1.5.3-6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12125 files and directories currently installed.) Preparing to unpack .../libblkid1_2.39.3-6.1_arm64.deb ... Unpacking libblkid1:arm64 (2.39.3-6.1) over (2.39.3-6) ... Setting up libblkid1:arm64 (2.39.3-6.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12125 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-6.1_arm64.deb ... Unpacking libmount1:arm64 (2.39.3-6.1) over (2.39.3-6) ... Setting up libmount1:arm64 (2.39.3-6.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12125 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.39.3-6.1_arm64.deb ... Unpacking libsmartcols1:arm64 (2.39.3-6.1) over (2.39.3-6) ... Setting up libsmartcols1:arm64 (2.39.3-6.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12125 files and directories currently installed.) Preparing to unpack .../xz-utils_5.6.0-0.2_arm64.deb ... Unpacking xz-utils (5.6.0-0.2) over (5.4.5-0.3) ... Preparing to unpack .../dpkg-dev_1.22.5_all.deb ... Unpacking dpkg-dev (1.22.5) over (1.22.4) ... Preparing to unpack .../libdpkg-perl_1.22.5_all.deb ... Unpacking libdpkg-perl (1.22.5) over (1.22.4) ... Setting up libtirpc-common (1.3.4+ds-1.1) ... Setting up libgomp1:arm64 (14-20240221-2.1) ... Setting up gcc-13-base:arm64 (13.2.0-16.1) ... Setting up xz-utils (5.6.0-0.2) ... Setting up libatomic1:arm64 (14-20240221-2.1) ... Setting up libdpkg-perl (1.22.5) ... Setting up libubsan1:arm64 (14-20240221-2.1) ... Setting up libhwasan0:arm64 (14-20240221-2.1) ... Setting up libasan8:arm64 (14-20240221-2.1) ... Setting up libtsan2:arm64 (14-20240221-2.1) ... Setting up libc-dev-bin (2.37-15.1) ... Setting up libcc1-0:arm64 (14-20240221-2.1) ... Setting up liblsan0:arm64 (14-20240221-2.1) ... Setting up libitm1:arm64 (14-20240221-2.1) ... Setting up cpp-13-aarch64-linux-gnu (13.2.0-16.1) ... Setting up libtirpc3t64:arm64 (1.3.4+ds-1.1) ... Setting up dpkg-dev (1.22.5) ... Setting up libtirpc-dev:arm64 (1.3.4+ds-1.1) ... Setting up libgcc-13-dev:arm64 (13.2.0-16.1) ... Setting up libc6-dev:arm64 (2.37-15.1) ... Setting up libstdc++-13-dev:arm64 (13.2.0-16.1) ... Setting up cpp-13 (13.2.0-16.1) ... Setting up gcc-13-aarch64-linux-gnu (13.2.0-16.1) ... Setting up gcc-13 (13.2.0-16.1) ... Setting up g++-13-aarch64-linux-gnu (13.2.0-16.1) ... Setting up g++-13 (13.2.0-16.1) ... Processing triggers for libc-bin (2.37-15.1) ... +------------------------------------------------------------------------------+ | 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://mirror.einval.org/debian unstable/main fastml 3.11-4 (dsc) [1900 B] Get:2 http://mirror.einval.org/debian unstable/main fastml 3.11-4 (tar) [849 kB] Get:3 http://mirror.einval.org/debian unstable/main fastml 3.11-4 (diff) [10.2 kB] Fetched 861 kB in 0s (3181 kB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/fastml-TxSayE/fastml-3.11' with '<>' I: NOTICE: Log filtering will replace 'build/fastml-TxSayE' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 Filtered Build-Depends: debhelper-compat (= 13), libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386 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 [711 B] Get:5 copy:/<>/apt_archive ./ Packages [753 B] Fetched 2073 B in 0s (113 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... Execute external solver... The following packages were automatically installed and are no longer required: libcom-err2 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnsl-dev libnsl2 libtirpc-common libtirpc-dev libtirpc3t64 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bsdextrautils cpp-13-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-13-i686-linux-gnu g++-i686-linux-gnu gcc-13-base:i386 gcc-13-cross-base gcc-13-i686-linux-gnu gcc-13-i686-linux-gnu-base gcc-14-base:i386 gcc-14-cross-base gcc-i686-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:i386 libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfakeroot libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-13-dev:i386 libgcc-13-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgomp1:i386 libgomp1-i386-cross libicu72 libio-string-perl libitm1:i386 libitm1-i386-cross liblocale-gettext-perl libmagic-mgc libmagic1t64 libpam0t64 libpipeline1 libquadmath0:i386 libquadmath0-i386-cross libstdc++-13-dev:i386 libstdc++-13-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsub-override-perl libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-i386-cross m4 man-db po-debconf sensible-utils ucf util-linux 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-i686-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:i386 libc-l10n:i386 locales:i386 libnss-nis:i386 libnss-nisplus:i386 manpages-dev:i386 libpam-doc libstdc++-13-doc:i386 libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl dosfstools kbd util-linux-extra util-linux-locales Recommended packages: curl | wget | lynx libidn2-0:i386 libarchive-cpio-perl libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following packages will be REMOVED: libpam0g* The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-i686-linux-gnu bsdextrautils cpp-13-i686-linux-gnu cpp-i686-linux-gnu cross-config crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz fakeroot file g++-13-i686-linux-gnu g++-i686-linux-gnu gcc-13-base:i386 gcc-13-cross-base gcc-13-i686-linux-gnu gcc-13-i686-linux-gnu-base gcc-14-base:i386 gcc-14-cross-base gcc-i686-linux-gnu gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan8:i386 libasan8-i386-cross libatomic1:i386 libatomic1-i386-cross libc6:i386 libc6-dev:i386 libc6-dev-i386-cross libc6-i386-cross libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:i386 libcrypt1:i386 libdebhelper-perl libdebian-dpkgcross-perl libelf1 libfakeroot libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-13-dev:i386 libgcc-13-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgomp1:i386 libgomp1-i386-cross libicu72 libio-string-perl libitm1:i386 libitm1-i386-cross liblocale-gettext-perl libmagic-mgc libmagic1t64 libpam0t64 libpipeline1 libquadmath0:i386 libquadmath0-i386-cross libstdc++-13-dev:i386 libstdc++-13-dev-i386-cross libstdc++6:i386 libstdc++6-i386-cross libsub-override-perl libtool libubsan1:i386 libubsan1-i386-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev-i386-cross m4 man-db po-debconf sbuild-build-depends-main-dummy:i386 sensible-utils ucf The following packages will be upgraded: util-linux 1 upgraded, 90 newly installed, 1 to remove and 0 not upgraded. Need to get 89.5 MB of archives. After this operation, 358 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [916 B] Get:2 http://mirror.einval.org/debian unstable/main arm64 libpam0t64 arm64 1.5.3-4 [66.1 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 util-linux arm64 2.39.3-6.1 [1201 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-6+b1 [15.0 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-2.1 [314 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-2.1 [100 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.45-2.1 [43.0 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-3 [1127 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.39.3-6.1 [90.3 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-1+b2 [36.7 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.12.0-3 [1385 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 gcc-13-i686-linux-gnu-base arm64 13.2.0-12cross1 [42.6 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 cpp-13-i686-linux-gnu arm64 13.2.0-12cross1 [9276 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 cpp-i686-linux-gnu arm64 4:13.2.0-7 [4720 B] Get:24 http://mirror.einval.org/debian unstable/main arm64 cross-config all 2.6.20 [16.3 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 binutils-i686-linux-gnu arm64 2.42-3 [2372 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 gcc-13-cross-base all 13.2.0-12cross1 [38.1 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 gcc-14-cross-base all 14-20240127-1cross1 [37.9 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libc6-i386-cross all 2.37-12cross1 [1339 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-i386-cross all 14-20240127-1cross1 [69.3 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libgomp1-i386-cross all 14-20240127-1cross1 [135 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libitm1-i386-cross all 14-20240127-1cross1 [26.7 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libatomic1-i386-cross all 14-20240127-1cross1 [7280 B] Get:33 http://mirror.einval.org/debian unstable/main arm64 libasan8-i386-cross all 14-20240127-1cross1 [2602 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-i386-cross all 14-20240127-1cross1 [719 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libubsan1-i386-cross all 14-20240127-1cross1 [1050 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-i386-cross all 14-20240127-1cross1 [233 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libgcc-13-dev-i386-cross all 13.2.0-12cross1 [2497 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 gcc-13-i686-linux-gnu arm64 13.2.0-12cross1 [17.8 MB] Get:39 http://mirror.einval.org/debian unstable/main arm64 gcc-i686-linux-gnu arm64 4:13.2.0-7 [1444 B] Get:40 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-i386-cross all 6.5.8-1cross1 [2014 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-i386-cross all 2.37-12cross1 [1716 kB] Get:42 http://mirror.einval.org/debian unstable/main arm64 libstdc++-13-dev-i386-cross all 13.2.0-12cross1 [2276 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 g++-13-i686-linux-gnu arm64 13.2.0-12cross1 [10.1 MB] Get:44 http://mirror.einval.org/debian unstable/main arm64 g++-i686-linux-gnu arm64 4:13.2.0-7 [1196 B] Get:45 http://mirror.einval.org/debian unstable/main arm64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b2 [624 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1+b2 [299 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libyaml-perl all 1.31-1 [64.8 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 dpkg-cross all 2.6.20 [25.8 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-i386 all 12.10 [3480 B] Get:61 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.14.1 [85.6 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:68 http://mirror.einval.org/debian unstable/main arm64 libelf1 arm64 0.190-1+b1 [175 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1 [101 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.14.1 [890 kB] Get:74 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.33-1 [28.3 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.33-1 [73.5 kB] Get:76 http://mirror.einval.org/debian unstable/main i386 gcc-13-base i386 13.2.0-16.1 [43.3 kB] Get:77 http://mirror.einval.org/debian unstable/main i386 gcc-14-base i386 14-20240221-2.1 [42.8 kB] Get:78 http://mirror.einval.org/debian unstable/main i386 libgcc-s1 i386 14-20240221-2.1 [69.9 kB] Get:79 http://mirror.einval.org/debian unstable/main i386 libc6 i386 2.37-15.1 [2625 kB] Get:80 http://mirror.einval.org/debian unstable/main i386 libasan8 i386 14-20240221-2.1 [2605 kB] Get:81 http://mirror.einval.org/debian unstable/main i386 libatomic1 i386 14-20240221-2.1 [7556 B] Get:82 http://mirror.einval.org/debian unstable/main i386 libcrypt1 i386 1:4.4.36-4 [95.7 kB] Get:83 http://mirror.einval.org/debian unstable/main i386 libcrypt-dev i386 1:4.4.36-4 [125 kB] Get:84 http://mirror.einval.org/debian unstable/main i386 libc6-dev i386 2.37-15.1 [1721 kB] Get:85 http://mirror.einval.org/debian unstable/main i386 libgomp1 i386 14-20240221-2.1 [138 kB] Get:86 http://mirror.einval.org/debian unstable/main i386 libitm1 i386 14-20240221-2.1 [27.2 kB] Get:87 http://mirror.einval.org/debian unstable/main i386 libstdc++6 i386 14-20240221-2.1 [765 kB] Get:88 http://mirror.einval.org/debian unstable/main i386 libubsan1 i386 14-20240221-2.1 [1050 kB] Get:89 http://mirror.einval.org/debian unstable/main i386 libquadmath0 i386 14-20240221-2.1 [233 kB] Get:90 http://mirror.einval.org/debian unstable/main i386 libgcc-13-dev i386 13.2.0-16.1 [2497 kB] Get:91 http://mirror.einval.org/debian unstable/main i386 libstdc++-13-dev i386 13.2.0-16.1 [2272 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 89.5 MB in 1s (86.2 MB/s) Selecting previously unselected package libpam0t64:arm64. (Reading database ... 12063 files and directories currently installed.) Preparing to unpack .../libpam0t64_1.5.3-4_arm64.deb ... Adding 'diversion of /lib/aarch64-linux-gnu/libpam.so.0 to /lib/aarch64-linux-gnu/libpam.so.0.usr-is-merged by libpam0t64' Adding 'diversion of /lib/aarch64-linux-gnu/libpam.so.0.85.1 to /lib/aarch64-linux-gnu/libpam.so.0.85.1.usr-is-merged by libpam0t64' Adding 'diversion of /lib/aarch64-linux-gnu/libpam_misc.so.0 to /lib/aarch64-linux-gnu/libpam_misc.so.0.usr-is-merged by libpam0t64' Adding 'diversion of /lib/aarch64-linux-gnu/libpam_misc.so.0.82.1 to /lib/aarch64-linux-gnu/libpam_misc.so.0.82.1.usr-is-merged by libpam0t64' Adding 'diversion of /lib/aarch64-linux-gnu/libpamc.so.0 to /lib/aarch64-linux-gnu/libpamc.so.0.usr-is-merged by libpam0t64' Adding 'diversion of /lib/aarch64-linux-gnu/libpamc.so.0.82.1 to /lib/aarch64-linux-gnu/libpamc.so.0.82.1.usr-is-merged by libpam0t64' Unpacking libpam0t64:arm64 (1.5.3-4) ... Replacing files in old package libpam0g:arm64 (1.5.3-6) ... dpkg: libpam0g:arm64: dependency problems, but removing anyway as you requested: util-linux depends on libpam0g (>= 0.99.7.1); however: Package libpam0g:arm64 is to be removed. Package libpam0t64:arm64 which provides libpam0g is not configured yet. login depends on libpam0g (>= 0.99.7.1); however: Package libpam0g:arm64 is to be removed. Package libpam0t64:arm64 which provides libpam0g is not configured yet. libpam-modules-bin depends on libpam0g (>= 0.99.7.1); however: Package libpam0g:arm64 is to be removed. Package libpam0t64:arm64 which provides libpam0g is not configured yet. libpam-modules:arm64 depends on libpam0g (>= 1.4.1); however: Package libpam0g:arm64 is to be removed. Package libpam0t64:arm64 which provides libpam0g is not configured yet. (Reading database ... 12084 files and directories currently installed.) Removing libpam0g:arm64 (1.5.3-6) ... Setting up libpam0t64:arm64 (1.5.3-4) ... (Reading database ... 12075 files and directories currently installed.) Preparing to unpack .../util-linux_2.39.3-6.1_arm64.deb ... Unpacking util-linux (2.39.3-6.1) over (2.39.3-6) ... Setting up util-linux (2.39.3-6.1) ... Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12075 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-6+b1_arm64.deb ... Unpacking liblocale-gettext-perl (1.07-6+b1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.22_all.deb ... Unpacking sensible-utils (0.0.22) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-2.1_arm64.deb ... Unpacking libmagic-mgc (1:5.45-2.1) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../03-libmagic1t64_1%3a5.45-2.1_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.45-2.1) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.45-2.1_arm64.deb ... Unpacking file (1:5.45-2.1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../05-gettext-base_0.21-14+b1_arm64.deb ... Unpacking gettext-base (0.21-14+b1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../06-libuchardet0_0.0.8-1+b1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b1) ... Selecting previously unselected package groff-base. Preparing to unpack .../07-groff-base_1.23.0-3_arm64.deb ... Unpacking groff-base (1.23.0-3) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../08-bsdextrautils_2.39.3-6.1_arm64.deb ... Unpacking bsdextrautils (2.39.3-6.1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../09-libpipeline1_1.5.7-1+b2_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1+b2) ... Selecting previously unselected package man-db. Preparing to unpack .../10-man-db_2.12.0-3_arm64.deb ... Unpacking man-db (2.12.0-3) ... Selecting previously unselected package ucf. Preparing to unpack .../11-ucf_3.0043+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0043+nmu1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_arm64.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.21-14_all.deb ... Unpacking autopoint (0.21-14) ... Selecting previously unselected package gcc-13-i686-linux-gnu-base:arm64. Preparing to unpack .../17-gcc-13-i686-linux-gnu-base_13.2.0-12cross1_arm64.deb ... Unpacking gcc-13-i686-linux-gnu-base:arm64 (13.2.0-12cross1) ... Selecting previously unselected package cpp-13-i686-linux-gnu. Preparing to unpack .../18-cpp-13-i686-linux-gnu_13.2.0-12cross1_arm64.deb ... Unpacking cpp-13-i686-linux-gnu (13.2.0-12cross1) ... Selecting previously unselected package cpp-i686-linux-gnu. Preparing to unpack .../19-cpp-i686-linux-gnu_4%3a13.2.0-7_arm64.deb ... Unpacking cpp-i686-linux-gnu (4:13.2.0-7) ... Selecting previously unselected package cross-config. Preparing to unpack .../20-cross-config_2.6.20_all.deb ... Unpacking cross-config (2.6.20) ... Selecting previously unselected package binutils-i686-linux-gnu. Preparing to unpack .../21-binutils-i686-linux-gnu_2.42-3_arm64.deb ... Unpacking binutils-i686-linux-gnu (2.42-3) ... Selecting previously unselected package gcc-13-cross-base. Preparing to unpack .../22-gcc-13-cross-base_13.2.0-12cross1_all.deb ... Unpacking gcc-13-cross-base (13.2.0-12cross1) ... Selecting previously unselected package gcc-14-cross-base. Preparing to unpack .../23-gcc-14-cross-base_14-20240127-1cross1_all.deb ... Unpacking gcc-14-cross-base (14-20240127-1cross1) ... Selecting previously unselected package libc6-i386-cross. Preparing to unpack .../24-libc6-i386-cross_2.37-12cross1_all.deb ... Unpacking libc6-i386-cross (2.37-12cross1) ... Selecting previously unselected package libgcc-s1-i386-cross. Preparing to unpack .../25-libgcc-s1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libgcc-s1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libgomp1-i386-cross. Preparing to unpack .../26-libgomp1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libgomp1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libitm1-i386-cross. Preparing to unpack .../27-libitm1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libitm1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libatomic1-i386-cross. Preparing to unpack .../28-libatomic1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libatomic1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libasan8-i386-cross. Preparing to unpack .../29-libasan8-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libasan8-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libstdc++6-i386-cross. Preparing to unpack .../30-libstdc++6-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libstdc++6-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libubsan1-i386-cross. Preparing to unpack .../31-libubsan1-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libubsan1-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libquadmath0-i386-cross. Preparing to unpack .../32-libquadmath0-i386-cross_14-20240127-1cross1_all.deb ... Unpacking libquadmath0-i386-cross (14-20240127-1cross1) ... Selecting previously unselected package libgcc-13-dev-i386-cross. Preparing to unpack .../33-libgcc-13-dev-i386-cross_13.2.0-12cross1_all.deb ... Unpacking libgcc-13-dev-i386-cross (13.2.0-12cross1) ... Selecting previously unselected package gcc-13-i686-linux-gnu. Preparing to unpack .../34-gcc-13-i686-linux-gnu_13.2.0-12cross1_arm64.deb ... Unpacking gcc-13-i686-linux-gnu (13.2.0-12cross1) ... Selecting previously unselected package gcc-i686-linux-gnu. Preparing to unpack .../35-gcc-i686-linux-gnu_4%3a13.2.0-7_arm64.deb ... Unpacking gcc-i686-linux-gnu (4:13.2.0-7) ... Selecting previously unselected package linux-libc-dev-i386-cross. Preparing to unpack .../36-linux-libc-dev-i386-cross_6.5.8-1cross1_all.deb ... Unpacking linux-libc-dev-i386-cross (6.5.8-1cross1) ... Selecting previously unselected package libc6-dev-i386-cross. Preparing to unpack .../37-libc6-dev-i386-cross_2.37-12cross1_all.deb ... Unpacking libc6-dev-i386-cross (2.37-12cross1) ... Selecting previously unselected package libstdc++-13-dev-i386-cross. Preparing to unpack .../38-libstdc++-13-dev-i386-cross_13.2.0-12cross1_all.deb ... Unpacking libstdc++-13-dev-i386-cross (13.2.0-12cross1) ... Selecting previously unselected package g++-13-i686-linux-gnu. Preparing to unpack .../39-g++-13-i686-linux-gnu_13.2.0-12cross1_arm64.deb ... Unpacking g++-13-i686-linux-gnu (13.2.0-12cross1) ... Selecting previously unselected package g++-i686-linux-gnu. Preparing to unpack .../40-g++-i686-linux-gnu_4%3a13.2.0-7_arm64.deb ... Unpacking g++-i686-linux-gnu (4:13.2.0-7) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../41-libconfig-inifiles-perl_3.000003-2_all.deb ... Unpacking libconfig-inifiles-perl (3.000003-2) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../42-libio-string-perl_1.08-4_all.deb ... Unpacking libio-string-perl (1.08-4) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../43-libicu72_72.1-4+b1_arm64.deb ... Unpacking libicu72:arm64 (72.1-4+b1) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../44-libxml2_2.9.14+dfsg-1.3+b2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../45-libxml-namespacesupport-perl_1.12-2_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-2) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../46-libxml-sax-base-perl_1.09-3_all.deb ... Unpacking libxml-sax-base-perl (1.09-3) ... Selecting previously unselected package libxml-sax-perl. Preparing to unpack .../47-libxml-sax-perl_1.02+dfsg-3_all.deb ... Unpacking libxml-sax-perl (1.02+dfsg-3) ... Selecting previously unselected package libxml-libxml-perl. Preparing to unpack .../48-libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b2_arm64.deb ... Unpacking libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b2) ... Selecting previously unselected package libxml-simple-perl. Preparing to unpack .../49-libxml-simple-perl_2.25-2_all.deb ... Unpacking libxml-simple-perl (2.25-2) ... Selecting previously unselected package libyaml-perl. Preparing to unpack .../50-libyaml-perl_1.31-1_all.deb ... Unpacking libyaml-perl (1.31-1) ... Selecting previously unselected package libconfig-auto-perl. Preparing to unpack .../51-libconfig-auto-perl_0.44-2_all.deb ... Unpacking libconfig-auto-perl (0.44-2) ... Selecting previously unselected package libfile-which-perl. Preparing to unpack .../52-libfile-which-perl_1.27-2_all.deb ... Unpacking libfile-which-perl (1.27-2) ... Selecting previously unselected package libfile-homedir-perl. Preparing to unpack .../53-libfile-homedir-perl_1.006-2_all.deb ... Unpacking libfile-homedir-perl (1.006-2) ... Selecting previously unselected package libdebian-dpkgcross-perl. Preparing to unpack .../54-libdebian-dpkgcross-perl_2.6.20_all.deb ... Unpacking libdebian-dpkgcross-perl (2.6.20) ... Selecting previously unselected package dpkg-cross. Preparing to unpack .../55-dpkg-cross_2.6.20_all.deb ... Unpacking dpkg-cross (2.6.20) ... Selecting previously unselected package crossbuild-essential-i386. Preparing to unpack .../56-crossbuild-essential-i386_12.10_all.deb ... Unpacking crossbuild-essential-i386 (12.10) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../57-libdebhelper-perl_13.14.1_all.deb ... Unpacking libdebhelper-perl (13.14.1) ... Selecting previously unselected package libtool. Preparing to unpack .../58-libtool_2.4.7-7_all.deb ... Unpacking libtool (2.4.7-7) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../59-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../60-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libsub-override-perl. Preparing to unpack .../61-libsub-override-perl_0.10-1_all.deb ... Unpacking libsub-override-perl (0.10-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../62-libfile-stripnondeterminism-perl_1.13.1-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.13.1-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../63-dh-strip-nondeterminism_1.13.1-1_all.deb ... Unpacking dh-strip-nondeterminism (1.13.1-1) ... Selecting previously unselected package libelf1:arm64. Preparing to unpack .../64-libelf1_0.190-1+b1_arm64.deb ... Unpacking libelf1:arm64 (0.190-1+b1) ... Selecting previously unselected package dwz. Preparing to unpack .../65-dwz_0.15-1_arm64.deb ... Unpacking dwz (0.15-1) ... Selecting previously unselected package gettext. Preparing to unpack .../66-gettext_0.21-14+b1_arm64.deb ... Unpacking gettext (0.21-14+b1) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../67-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../68-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../69-debhelper_13.14.1_all.deb ... Unpacking debhelper (13.14.1) ... Selecting previously unselected package libfakeroot:arm64. Preparing to unpack .../70-libfakeroot_1.33-1_arm64.deb ... Unpacking libfakeroot:arm64 (1.33-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../71-fakeroot_1.33-1_arm64.deb ... Unpacking fakeroot (1.33-1) ... Selecting previously unselected package gcc-13-base:i386. Preparing to unpack .../72-gcc-13-base_13.2.0-16.1_i386.deb ... Unpacking gcc-13-base:i386 (13.2.0-16.1) ... Selecting previously unselected package gcc-14-base:i386. Preparing to unpack .../73-gcc-14-base_14-20240221-2.1_i386.deb ... Unpacking gcc-14-base:i386 (14-20240221-2.1) ... Selecting previously unselected package libgcc-s1:i386. Preparing to unpack .../74-libgcc-s1_14-20240221-2.1_i386.deb ... Unpacking libgcc-s1:i386 (14-20240221-2.1) ... Selecting previously unselected package libc6:i386. Preparing to unpack .../75-libc6_2.37-15.1_i386.deb ... Unpacking libc6:i386 (2.37-15.1) ... Selecting previously unselected package libasan8:i386. Preparing to unpack .../76-libasan8_14-20240221-2.1_i386.deb ... Unpacking libasan8:i386 (14-20240221-2.1) ... Selecting previously unselected package libatomic1:i386. Preparing to unpack .../77-libatomic1_14-20240221-2.1_i386.deb ... Unpacking libatomic1:i386 (14-20240221-2.1) ... Selecting previously unselected package libcrypt1:i386. Preparing to unpack .../78-libcrypt1_1%3a4.4.36-4_i386.deb ... Unpacking libcrypt1:i386 (1:4.4.36-4) ... Selecting previously unselected package libcrypt-dev:i386. Preparing to unpack .../79-libcrypt-dev_1%3a4.4.36-4_i386.deb ... Unpacking libcrypt-dev:i386 (1:4.4.36-4) ... Selecting previously unselected package libc6-dev:i386. Preparing to unpack .../80-libc6-dev_2.37-15.1_i386.deb ... Unpacking libc6-dev:i386 (2.37-15.1) ... Selecting previously unselected package libgomp1:i386. Preparing to unpack .../81-libgomp1_14-20240221-2.1_i386.deb ... Unpacking libgomp1:i386 (14-20240221-2.1) ... Selecting previously unselected package libitm1:i386. Preparing to unpack .../82-libitm1_14-20240221-2.1_i386.deb ... Unpacking libitm1:i386 (14-20240221-2.1) ... Selecting previously unselected package libstdc++6:i386. Preparing to unpack .../83-libstdc++6_14-20240221-2.1_i386.deb ... Unpacking libstdc++6:i386 (14-20240221-2.1) ... Selecting previously unselected package libubsan1:i386. Preparing to unpack .../84-libubsan1_14-20240221-2.1_i386.deb ... Unpacking libubsan1:i386 (14-20240221-2.1) ... Selecting previously unselected package libquadmath0:i386. Preparing to unpack .../85-libquadmath0_14-20240221-2.1_i386.deb ... Unpacking libquadmath0:i386 (14-20240221-2.1) ... Selecting previously unselected package libgcc-13-dev:i386. Preparing to unpack .../86-libgcc-13-dev_13.2.0-16.1_i386.deb ... Unpacking libgcc-13-dev:i386 (13.2.0-16.1) ... Selecting previously unselected package libstdc++-13-dev:i386. Preparing to unpack .../87-libstdc++-13-dev_13.2.0-16.1_i386.deb ... Unpacking libstdc++-13-dev:i386 (13.2.0-16.1) ... Selecting previously unselected package sbuild-build-depends-main-dummy:i386. Preparing to unpack .../88-sbuild-build-depends-main-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Setting up libconfig-inifiles-perl (3.000003-2) ... Setting up libpipeline1:arm64 (1.5.7-1+b2) ... Setting up libfile-which-perl (1.27-2) ... Setting up libicu72:arm64 (72.1-4+b1) ... Setting up bsdextrautils (2.39.3-6.1) ... Setting up libmagic-mgc (1:5.45-2.1) ... Setting up gcc-14-base:i386 (14-20240221-2.1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up binutils-i686-linux-gnu (2.42-3) ... Setting up libdebhelper-perl (13.14.1) ... Setting up libmagic1t64:arm64 (1:5.45-2.1) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-14+b1) ... Setting up m4 (1.4.19-4) ... Setting up gcc-14-cross-base (14-20240127-1cross1) ... Setting up file (1:5.45-2.1) ... Setting up libyaml-perl (1.31-1) ... Setting up libfakeroot:arm64 (1.33-1) ... Setting up fakeroot (1.33-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up linux-libc-dev-i386-cross (6.5.8-1cross1) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up gcc-13-base:i386 (13.2.0-16.1) ... Setting up gcc-13-cross-base (13.2.0-12cross1) ... Setting up autopoint (0.21-14) ... Setting up autoconf (2.71-3) ... Setting up sensible-utils (0.0.22) ... Setting up libuchardet0:arm64 (0.0.8-1+b1) ... Setting up libc6-i386-cross (2.37-12cross1) ... Setting up libsub-override-perl (0.10-1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up gcc-13-i686-linux-gnu-base:arm64 (13.2.0-12cross1) ... Setting up cpp-13-i686-linux-gnu (13.2.0-12cross1) ... Setting up libquadmath0-i386-cross (14-20240127-1cross1) ... Setting up libelf1:arm64 (0.190-1+b1) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.3+b2) ... Setting up liblocale-gettext-perl (1.07-6+b1) ... 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+b1) ... Setting up libtool (2.4.7-7) ... Setting up libatomic1-i386-cross (14-20240127-1cross1) ... Setting up libgomp1-i386-cross (14-20240127-1cross1) ... Setting up libc6-dev-i386-cross (2.37-12cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libgcc-s1-i386-cross (14-20240127-1cross1) ... Setting up dh-autoreconf (20) ... Setting up libitm1-i386-cross (14-20240127-1cross1) ... Setting up ucf (3.0043+nmu1) ... 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 cpp-i686-linux-gnu (4:13.2.0-7) ... 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 libasan8-i386-cross (14-20240127-1cross1) ... Setting up libstdc++6-i386-cross (14-20240127-1cross1) ... 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 debhelper (13.14.1) ... Setting up libubsan1-i386-cross (14-20240127-1cross1) ... Setting up libxml-simple-perl (2.25-2) ... Setting up libgcc-13-dev-i386-cross (13.2.0-12cross1) ... Setting up gcc-13-i686-linux-gnu (13.2.0-12cross1) ... Setting up libstdc++-13-dev-i386-cross (13.2.0-12cross1) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up gcc-i686-linux-gnu (4:13.2.0-7) ... Setting up g++-13-i686-linux-gnu (13.2.0-12cross1) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up g++-i686-linux-gnu (4:13.2.0-7) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-i386 (12.10) ... Setting up libgcc-s1:i386 (14-20240221-2.1) ... Setting up libc6:i386 (2.37-15.1) ... Setting up libasan8:i386 (14-20240221-2.1) ... Setting up libstdc++6:i386 (14-20240221-2.1) ... Setting up libitm1:i386 (14-20240221-2.1) ... Setting up libcrypt1:i386 (1:4.4.36-4) ... Setting up libgomp1:i386 (14-20240221-2.1) ... Setting up libquadmath0:i386 (14-20240221-2.1) ... Setting up libatomic1:i386 (14-20240221-2.1) ... Setting up libubsan1:i386 (14-20240221-2.1) ... Setting up libgcc-13-dev:i386 (13.2.0-16.1) ... Setting up libcrypt-dev:i386 (1:4.4.36-4) ... Setting up libc6-dev:i386 (2.37-15.1) ... Setting up libstdc++-13-dev:i386 (13.2.0-16.1) ... Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.37-15.1) ... (Reading database ... 18309 files and directories currently installed.) Purging configuration files for libpam0g:arm64 (1.5.3-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (i386 included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-7-arm64 #1 SMP Debian 6.1.20-1 (2023-03-19) arm64 (aarch64) Toolchain package versions: binutils_2.42-3 dpkg-dev_1.22.5 g++-13_13.2.0-16.1 gcc-13_13.2.0-16.1 libc6-dev_2.37-15.1 libstdc++-13-dev_13.2.0-16.1 libstdc++-13-dev-i386-cross_13.2.0-12cross1 libstdc++6_14-20240221-2.1 libstdc++6-i386-cross_14-20240127-1cross1 linux-libc-dev_6.6.15-2 Package versions: apt_2.7.13+b1 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_2.42-3 binutils-aarch64-linux-gnu_2.42-3 binutils-common_2.42-3 binutils-i686-linux-gnu_2.42-3 bsdextrautils_2.39.3-6.1 bsdutils_1:2.39.3-6.1 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.4-3 cpp_4:13.2.0-7 cpp-13_13.2.0-16.1 cpp-13-aarch64-linux-gnu_13.2.0-16.1 cpp-13-i686-linux-gnu_13.2.0-12cross1 cpp-aarch64-linux-gnu_4:13.2.0-7 cpp-i686-linux-gnu_4:13.2.0-7 cross-config_2.6.20 crossbuild-essential-i386_12.10 dash_0.5.12-6 debconf_1.5.86 debhelper_13.14.1 debian-archive-keyring_2023.4 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.5 dpkg-cross_2.6.20 dpkg-dev_1.22.5 dwz_0.15-1 fakeroot_1.33-1 file_1:5.45-2.1 findutils_4.9.0-5 g++_4:13.2.0-7 g++-13_13.2.0-16.1 g++-13-aarch64-linux-gnu_13.2.0-16.1 g++-13-i686-linux-gnu_13.2.0-12cross1 g++-aarch64-linux-gnu_4:13.2.0-7 g++-i686-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-16.1 gcc-13-aarch64-linux-gnu_13.2.0-16.1 gcc-13-base_13.2.0-16.1 gcc-13-cross-base_13.2.0-12cross1 gcc-13-i686-linux-gnu_13.2.0-12cross1 gcc-13-i686-linux-gnu-base_13.2.0-12cross1 gcc-14-base_14-20240221-2.1 gcc-14-cross-base_14-20240127-1cross1 gcc-aarch64-linux-gnu_4:13.2.0-7 gcc-i686-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 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-pkg6.0t64_2.7.13+b1 libarchive-zip-perl_1.68-1 libasan8_14-20240221-2.1 libasan8-i386-cross_14-20240127-1cross1 libatomic1_14-20240221-2.1 libatomic1-i386-cross_14-20240127-1cross1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-3 libblkid1_2.39.3-6.1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-15.1 libc-dev-bin_2.37-15.1 libc6_2.37-15.1 libc6-dev_2.37-15.1 libc6-dev-i386-cross_2.37-12cross1 libc6-i386-cross_2.37-12cross1 libcap-ng0_0.8.4-2 libcap2_1:2.66-5 libcc1-0_14-20240221-2.1 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_2.42-3 libctf0_2.42-3 libdb5.3_5.3.28+dfsg2-4+b1 libdebconfclient0_0.271+b1 libdebhelper-perl_13.14.1 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.22.5 libelf1_0.190-1+b1 libfakeroot_1.33-1 libffi8_3.4.6-1 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-13-dev_13.2.0-16.1 libgcc-13-dev-i386-cross_13.2.0-12cross1 libgcc-s1_14-20240221-2.1 libgcc-s1-i386-cross_14-20240127-1cross1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5+b1 libgdbm6_1.23-5+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.3-1.1 libgomp1_14-20240221-2.1 libgomp1-i386-cross_14-20240127-1cross1 libgpg-error0_1.47-3 libgprofng0_2.42-3 libgssapi-krb5-2_1.20.1-5+b1 libhogweed6_3.9.1-2+b1 libhwasan0_14-20240221-2.1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libio-string-perl_1.08-4 libisl23_0.26-3+b2 libitm1_14-20240221-2.1 libitm1-i386-cross_14-20240127-1cross1 libjansson4_2.14-2+b2 libk5crypto3_1.20.1-5+b1 libkeyutils1_1.6.3-3 libkrb5-3_1.20.1-5+b1 libkrb5support0_1.20.1-5+b1 liblocale-gettext-perl_1.07-6+b1 liblsan0_14-20240221-2.1 liblz4-1_1.9.4-1+b2 liblzma5_5.6.0-0.2 libmagic-mgc_1:5.45-2.1 libmagic1t64_1:5.45-2.1 libmd0_1.1.0-2 libmount1_2.39.3-6.1 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libnettle8_3.9.1-2+b1 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_1.5.3-6 libpam-modules-bin_1.5.3-6 libpam-runtime_1.5.3-6 libpam0t64_1.5.3-4 libpcre2-8-0_10.42-4+b1 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1+b2 libquadmath0_14-20240221-2.1 libquadmath0-i386-cross_14-20240127-1cross1 libseccomp2_2.5.5-1 libselinux1_3.5-2 libsframe1_2.42-3 libsmartcols1_2.39.3-6.1 libssl3_3.1.5-1 libstdc++-13-dev_13.2.0-16.1 libstdc++-13-dev-i386-cross_13.2.0-12cross1 libstdc++6_14-20240221-2.1 libstdc++6-i386-cross_14-20240127-1cross1 libsub-override-perl_0.10-1 libsystemd0_255.4-1 libtasn1-6_4.19.0-3+b2 libtext-glob-perl_0.11-3 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1.1 libtirpc-dev_1.3.4+ds-1.1 libtirpc3t64_1.3.4+ds-1.1 libtool_2.4.7-7 libtsan2_14-20240221-2.1 libubsan1_14-20240221-2.1 libubsan1-i386-cross_14-20240127-1cross1 libuchardet0_0.0.8-1+b1 libudev1_255.4-1 libunistring5_1.1-2 libuuid1t64_2.39.3-6.1 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+b1 libyaml-perl_1.31-1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.6.15-2 linux-libc-dev-i386-cross_6.5.8-1cross1 login_1:4.13+dfsg1-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 patch_2.7.6-7 perl_5.38.2-3 perl-base_5.38.2-3 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_0.0.22 sysvinit-utils_3.08-7 tar_1.35+dfsg-3 ucf_3.0043+nmu1 usrmerge_39 util-linux_2.39.3-6.1 xz-utils_5.6.0-0.2 zlib1g_1:1.3.dfsg-3.1 +------------------------------------------------------------------------------+ | 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.i386 DEB_BUILD_OPTIONS=nocheck HOME=/var/lib/sbuild LANG=en_GB.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut OLDPWD=/ PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/<> SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -ai386 -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 i686-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 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=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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; | ^~~~ i686-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 | ^~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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): | ^~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 i686-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/i686-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/i686-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/i686-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/i686-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/i686-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/i686-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/i686-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; | ^~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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): | ^~~~~~~~~~~~~~~~ i686-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 i686-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 i686-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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 i686-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; | ^~~~~~~~~~~~~~~ i686-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 i686-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 i686-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 i686-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; | ^~~~~~~~~~~~~~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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/i686-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 | ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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)) | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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(); | ^~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 i686-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(); | ^~~~~~~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 i686-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, | ^~~~~~~~~~~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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) : | ^~~~~~~~~~~~~~~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 { | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 i686-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 i686-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) | ^~~~~~~~~~~~ i686-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; | ^~~~~ i686-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 i686-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/i686-linux-gnu/include/c++/13/i686-linux-gnu/bits/c++allocator.h:33, from /usr/i686-linux-gnu/include/c++/13/bits/allocator.h:46, from /usr/i686-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/i686-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/i686-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/i686-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/i686-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/i686-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/i686-linux-gnu/include/c++/13/vector:72: /usr/i686-linux-gnu/include/c++/13/bits/vector.tcc: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’: /usr/i686-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/i686-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/i686-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/i686-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/i686-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/i686-linux-gnu/include/c++/13/bits/vector.tcc: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’: /usr/i686-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; | ^~~~~ i686-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; | ^~~~ i686-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))); | ^~~~~~~~ i686-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))); | ^~~~~~~~ i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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 i686-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; | ^~~~~~ i686-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, | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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 i686-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 i686-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() { | ^~~~~~~~~~~~~~~~~~~ i686-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() { | ^~~~~~~~~~~~~~~~~~~ i686-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 i686-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 i686-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() { | ^~~~~~~~~~~~~~~~~~~ i686-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() { | ^~~~~~~~~~~~~~~~~~~ i686-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() { | ^~~~~~~~~~~~~~~~~~~ i686-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() { | ^~~~~~~~~~~~~~~~~~~ i686-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 ) : | ^~~~~~~~~~~ i686-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; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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; | ^~~~ i686-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; | ^~ i686-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 i686-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 i686-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 i686-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG -c -o gainLossOptions.o gainLossOptions.cpp gainLossOptions.cpp: In static member function ‘static gainLossOptions::optimizationLevel gainLossOptions::getOptimizationLevelTypeFromStr(const std::string&)’: gainLossOptions.cpp:2064:16: warning: ‘returnType’ may be used uninitialized [-Wmaybe-uninitialized] 2064 | return returnType; | ^~~~~~~~~~ gainLossOptions.cpp:2047:27: note: ‘returnType’ was declared here 2047 | optimizationLevel returnType; | ^~~~~~~~~~ gainLossOptions.cpp: In static member function ‘static gainLossOptions::costMatrixType gainLossOptions::getCostMatrixTypeFromStr(const std::string&)’: gainLossOptions.cpp:2111:16: warning: ‘returnType’ may be used uninitialized [-Wmaybe-uninitialized] 2111 | return returnType; | ^~~~~~~~~~ gainLossOptions.cpp:2098:24: note: ‘returnType’ was declared here 2098 | costMatrixType returnType; | ^~~~~~~~~~ gainLossOptions.cpp: In static member function ‘static gainLossOptions::simulationType gainLossOptions::getSimulationTypeFromStr(const std::string&)’: gainLossOptions.cpp:2419:16: warning: ‘returnType’ may be used uninitialized [-Wmaybe-uninitialized] 2419 | return returnType; | ^~~~~~~~~~ gainLossOptions.cpp:2396:24: note: ‘returnType’ was declared here 2396 | simulationType returnType; | ^~~~~~~~~~ i686-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/i686-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/i686-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/i686-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/i686-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; | ^~~ i686-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; | ^~~ i686-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; | ^~~~~~~~~ i686-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; | ^~~~~~~~~ i686-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): | ^~~~~~~~~~~~~ i686-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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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/i686-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/i686-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/i686-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/i686-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; | ^~~ i686-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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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; | ^~~ i686-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 i686-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; | ^~~~~~~~~~~~ i686-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): | ^~~~~~~~~~~~~~~ i686-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, | ^~~~~~~~~~~~~ i686-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) | ^~~~~~~~~~~~~~~~~~~~~~~~~~ i686-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; | ^~~~~~ i686-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) | ^~~~ i686-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 i686-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 i686-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; | ^~~~~~~~~ i686-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 i686-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 i686-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 i686-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; | ^~~~~~~~~~~~~~~~~ i686-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 i686-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_i386.deb'. dpkg-deb: building package 'fastml-dbgsym' in '../fastml-dbgsym_3.11-4_i386.deb'. dpkg-genbuildinfo --build=any -O../fastml_3.11-4_i386.buildinfo dpkg-genchanges --build=any -O../fastml_3.11-4_i386.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 2024-03-01T20:20:34Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ fastml_3.11-4_i386.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: i386 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: d12d9762f4cbf6ad1a917be9f097b72ddc0d3cc9 17467756 fastml-dbgsym_3.11-4_i386.deb 578f7b5e4e59493bcbec41d803d474a193408df6 5170 fastml_3.11-4_i386.buildinfo 2369f68ec6d82460bd238c353a96963a9b60169d 962396 fastml_3.11-4_i386.deb Checksums-Sha256: ee82fa3b62ca80d16c202b9e75433689c6f46dbd234f3610dae276e3b5eeae90 17467756 fastml-dbgsym_3.11-4_i386.deb 1293415e36b4f80bdaa7910d14ecabf73893da0a243cc92dd2f1196423cc7e5e 5170 fastml_3.11-4_i386.buildinfo 99ede30c56f0a6c8b7b40696afa173c418756a1afb357f030d60747dd0c171fb 962396 fastml_3.11-4_i386.deb Files: 5c7916b8f5a4f98740bf45457124d07e 17467756 debug optional fastml-dbgsym_3.11-4_i386.deb 0b733272664e2e6a49471ee02e6d1551 5170 science optional fastml_3.11-4_i386.buildinfo 39f2140bc46cf56f0b923d235ae49748 962396 science optional fastml_3.11-4_i386.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: fastml Binary: fastml fastml-dbgsym Architecture: i386 Version: 3.11-4 Checksums-Md5: 5c7916b8f5a4f98740bf45457124d07e 17467756 fastml-dbgsym_3.11-4_i386.deb 39f2140bc46cf56f0b923d235ae49748 962396 fastml_3.11-4_i386.deb Checksums-Sha1: d12d9762f4cbf6ad1a917be9f097b72ddc0d3cc9 17467756 fastml-dbgsym_3.11-4_i386.deb 2369f68ec6d82460bd238c353a96963a9b60169d 962396 fastml_3.11-4_i386.deb Checksums-Sha256: ee82fa3b62ca80d16c202b9e75433689c6f46dbd234f3610dae276e3b5eeae90 17467756 fastml-dbgsym_3.11-4_i386.deb 99ede30c56f0a6c8b7b40696afa173c418756a1afb357f030d60747dd0c171fb 962396 fastml_3.11-4_i386.deb Build-Origin: Debian Build-Architecture: arm64 Build-Date: Fri, 01 Mar 2024 20:20:33 +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 (= 2.42-3), binutils-aarch64-linux-gnu (= 2.42-3), binutils-common (= 2.42-3), bsdextrautils (= 2.39.3-6.1), bsdutils (= 1:2.39.3-6.1), build-essential (= 12.10), bzip2 (= 1.0.8-5+b2), coreutils (= 9.4-3), cpp (= 4:13.2.0-7), cpp-13 (= 13.2.0-16.1), cpp-13-aarch64-linux-gnu (= 13.2.0-16.1), cpp-aarch64-linux-gnu (= 4:13.2.0-7), dash (= 0.5.12-6), debconf (= 1.5.86), debhelper (= 13.14.1), debianutils (= 5.16), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.13.1-1), diffutils (= 1:3.10-1), dpkg (= 1.22.5), dpkg-dev (= 1.22.5), dwz (= 0.15-1), file (= 1:5.45-2.1), findutils (= 4.9.0-5), g++ (= 4:13.2.0-7), g++-13 (= 13.2.0-16.1), g++-13-aarch64-linux-gnu (= 13.2.0-16.1), g++-aarch64-linux-gnu (= 4:13.2.0-7), gcc (= 4:13.2.0-7), gcc-13 (= 13.2.0-16.1), gcc-13-aarch64-linux-gnu (= 13.2.0-16.1), gcc-13-base (= 13.2.0-16.1), gcc-14-base (= 14-20240221-2.1), gcc-aarch64-linux-gnu (= 4:13.2.0-7), gettext (= 0.21-14+b1), gettext-base (= 0.21-14+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), libarchive-zip-perl (= 1.68-1), libasan8 (= 14-20240221-2.1), libatomic1 (= 14-20240221-2.1), libattr1 (= 1:2.5.2-1), libaudit-common (= 1:3.1.2-2.1), libaudit1 (= 1:3.1.2-2.1), libbinutils (= 2.42-3), libblkid1 (= 2.39.3-6.1), libbz2-1.0 (= 1.0.8-5+b2), libc-bin (= 2.37-15.1), libc-dev-bin (= 2.37-15.1), libc6 (= 2.37-15.1), libc6-dev (= 2.37-15.1), libcap-ng0 (= 0.8.4-2), libcap2 (= 1:2.66-5), libcc1-0 (= 14-20240221-2.1), libcrypt-dev (= 1:4.4.36-4), libcrypt1 (= 1:4.4.36-4), libctf-nobfd0 (= 2.42-3), libctf0 (= 2.42-3), libdb5.3 (= 5.3.28+dfsg2-4+b1), libdebconfclient0 (= 0.271+b1), libdebhelper-perl (= 13.14.1), libdpkg-perl (= 1.22.5), libelf1 (= 0.190-1+b1), libfile-find-rule-perl (= 0.34-3), libfile-stripnondeterminism-perl (= 1.13.1-1), libgcc-13-dev (= 13.2.0-16.1), libgcc-s1 (= 14-20240221-2.1), libgcrypt20 (= 1.10.3-2), libgdbm-compat4 (= 1.23-5+b1), libgdbm6 (= 1.23-5+b1), libgmp10 (= 2:6.3.0+dfsg-2+b1), libgomp1 (= 14-20240221-2.1), libgpg-error0 (= 1.47-3), libgprofng0 (= 2.42-3), libhwasan0 (= 14-20240221-2.1), libicu72 (= 72.1-4+b1), libisl23 (= 0.26-3+b2), libitm1 (= 14-20240221-2.1), libjansson4 (= 2.14-2+b2), liblsan0 (= 14-20240221-2.1), liblz4-1 (= 1.9.4-1+b2), liblzma5 (= 5.6.0-0.2), libmagic-mgc (= 1:5.45-2.1), libmagic1t64 (= 1:5.45-2.1), libmd0 (= 1.1.0-2), libmount1 (= 2.39.3-6.1), libmpc3 (= 1.3.1-1+b2), libmpfr6 (= 4.2.1-1+b1), libnumber-compare-perl (= 0.03-3), libpam-modules (= 1.5.3-6), libpam-modules-bin (= 1.5.3-6), libpam-runtime (= 1.5.3-6), libpam0t64 (= 1.5.3-4), libpcre2-8-0 (= 10.42-4+b1), libperl5.38 (= 5.38.2-3), libpipeline1 (= 1.5.7-1+b2), libseccomp2 (= 2.5.5-1), libselinux1 (= 3.5-2), libsframe1 (= 2.42-3), libsmartcols1 (= 2.39.3-6.1), libssl3 (= 3.1.5-1), libstdc++-13-dev (= 13.2.0-16.1), libstdc++6 (= 14-20240221-2.1), libsub-override-perl (= 0.10-1), libsystemd0 (= 255.4-1), libtext-glob-perl (= 0.11-3), libtinfo6 (= 6.4+20240113-1), libtool (= 2.4.7-7), libtsan2 (= 14-20240221-2.1), libubsan1 (= 14-20240221-2.1), libuchardet0 (= 0.0.8-1+b1), libudev1 (= 255.4-1), libunistring5 (= 1.1-2), libuuid1t64 (= 2.39.3-6.1), libxml2 (= 2.9.14+dfsg-1.3+b2), libzstd1 (= 1.5.5+dfsg2-2), linux-libc-dev (= 6.6.15-2), login (= 1:4.13+dfsg1-4), m4 (= 1.4.19-4), make (= 4.3-4.1), man-db (= 2.12.0-3), mawk (= 1.3.4.20240123-1), ncurses-base (= 6.4+20240113-1), ncurses-bin (= 6.4+20240113-1), patch (= 2.7.6-7), perl (= 5.38.2-3), perl-base (= 5.38.2-3), perl-modules-5.38 (= 5.38.2-3), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.22), sysvinit-utils (= 3.08-7), tar (= 1.35+dfsg-3), usrmerge (= 39), util-linux (= 2.39.3-6.1), xz-utils (= 5.6.0-0.2), zlib1g (= 1:1.3.dfsg-3.1) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_GB.UTF-8" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1706113401" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ fastml-dbgsym_3.11-4_i386.deb ----------------------------- new Debian package, version 2.0. size 17467756 bytes: control archive=696 bytes. 447 bytes, 12 lines control 399 bytes, 4 lines md5sums Package: fastml-dbgsym Source: fastml Version: 3.11-4 Auto-Built-Package: debug-symbols Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 17476 Depends: fastml (= 3.11-4) Section: debug Priority: optional Description: debug symbols for fastml Build-Ids: 0fcd9c7bca7c7bd27cbeea659e06f5e0e398b3c9 e2487e228a0d363b9f415fe46e4e16b648671bc8 edaae3593cd20f2af4e9edcfd02ad20a751ab405 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/0f/ -rw-r--r-- root/root 6331056 2024-01-24 16:23 ./usr/lib/debug/.build-id/0f/cd9c7bca7c7bd27cbeea659e06f5e0e398b3c9.debug drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/.build-id/e2/ -rw-r--r-- root/root 1293012 2024-01-24 16:23 ./usr/lib/debug/.build-id/e2/487e228a0d363b9f415fe46e4e16b648671bc8.debug drwxr-xr-x root/root 0 2024-01-24 16:23 ./usr/lib/debug/.build-id/ed/ -rw-r--r-- root/root 9040684 2024-01-24 16:23 ./usr/lib/debug/.build-id/ed/aae3593cd20f2af4e9edcfd02ad20a751ab405.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/i386-linux-gnu/ -rw-r--r-- root/root 1214656 2024-01-24 16:23 ./usr/lib/debug/.dwz/i386-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_i386.deb ---------------------- new Debian package, version 2.0. size 962396 bytes: control archive=1244 bytes. 1433 bytes, 26 lines control 494 bytes, 8 lines md5sums Package: fastml Version: 3.11-4 Architecture: i386 Maintainer: Debian Med Packaging Team Installed-Size: 3547 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), 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 1246816 2024-01-24 16:23 ./usr/bin/fastml -rwxr-xr-x root/root 2053728 2024-01-24 16:23 ./usr/bin/gainLoss -rwxr-xr-x root/root 312928 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:arm64 Filtered Build-Depends: lintian:arm64 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 [1293 B] Get:5 copy:/<>/apt_archive ./ Packages [1370 B] Fetched 3278 B in 0s (186 kB/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 packages were automatically installed and are no longer required: libcom-err2 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnsl-dev libnsl2 libtirpc-common libtirpc-dev libtirpc3t64 Use 'apt autoremove' to remove them. 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 libssl3t64 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 packages will be REMOVED: libssl3* 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 libssl3t64 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:i386 t1utils unzip 0 upgraded, 127 newly installed, 1 to remove and 0 not upgraded. Need to get 15.1 MB of archives. After this operation, 53.3 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://mirror.einval.org/debian unstable/main arm64 libssl3t64 arm64 3.1.5-1.1 [1839 kB] Get:3 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB] Get:4 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-3.1 [69.2 kB] Get:5 http://mirror.einval.org/debian unstable/main arm64 openssl arm64 3.1.5-1.1 [1208 kB] Get:6 http://mirror.einval.org/debian unstable/main arm64 ca-certificates all 20240203 [158 kB] Get:7 http://mirror.einval.org/debian unstable/main arm64 diffstat arm64 1.65-1 [31.2 kB] Get:8 http://mirror.einval.org/debian unstable/main arm64 libassuan0 arm64 2.5.6-1 [47.3 kB] Get:9 http://mirror.einval.org/debian unstable/main arm64 libreadline8 arm64 8.2-3+b1 [157 kB] Get:10 http://mirror.einval.org/debian unstable/main arm64 gpgconf arm64 2.2.40-1.1+b1 [558 kB] Get:11 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.45.1-1 [835 kB] Get:12 http://mirror.einval.org/debian unstable/main arm64 gpg arm64 2.2.40-1.1+b1 [903 kB] Get:13 http://mirror.einval.org/debian unstable/main arm64 iso-codes all 4.16.0-1 [2936 kB] Get:14 http://mirror.einval.org/debian unstable/main arm64 libaliased-perl all 0.34-3 [13.5 kB] Get:15 http://mirror.einval.org/debian unstable/main arm64 libapt-pkg-perl arm64 0.1.40+b4 [63.8 kB] Get:16 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-op-check-perl arm64 0.22-2+b2 [10.7 kB] Get:17 http://mirror.einval.org/debian unstable/main arm64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:18 http://mirror.einval.org/debian unstable/main arm64 libdevel-callchecker-perl arm64 0.008-2+b1 [15.2 kB] Get:19 http://mirror.einval.org/debian unstable/main arm64 libparams-classify-perl arm64 0.015-2+b2 [22.3 kB] Get:20 http://mirror.einval.org/debian unstable/main arm64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:21 http://mirror.einval.org/debian unstable/main arm64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:22 http://mirror.einval.org/debian unstable/main arm64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:23 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:24 http://mirror.einval.org/debian unstable/main arm64 libvariable-magic-perl arm64 0.63-1+b2 [42.7 kB] Get:25 http://mirror.einval.org/debian unstable/main arm64 libb-hooks-endofscope-perl all 0.26-1 [19.6 kB] Get:26 http://mirror.einval.org/debian unstable/main arm64 libberkeleydb-perl arm64 0.64-2+b2 [120 kB] Get:27 http://mirror.einval.org/debian unstable/main arm64 libcapture-tiny-perl all 0.48-2 [24.6 kB] Get:28 http://mirror.einval.org/debian unstable/main arm64 libhtml-tagset-perl all 3.20-6 [11.7 kB] Get:29 http://mirror.einval.org/debian unstable/main arm64 liburi-perl all 5.27-1 [98.4 kB] Get:30 http://mirror.einval.org/debian unstable/main arm64 libhtml-parser-perl arm64 3.81-1+b1 [97.1 kB] Get:31 http://mirror.einval.org/debian unstable/main arm64 libcgi-pm-perl all 4.61-1 [217 kB] Get:32 http://mirror.einval.org/debian unstable/main arm64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:33 http://mirror.einval.org/debian unstable/main arm64 libclass-method-modifiers-perl all 2.15-1 [18.0 kB] Get:34 http://mirror.einval.org/debian unstable/main arm64 libclass-xsaccessor-perl arm64 1.19-4+b2 [35.2 kB] Get:35 http://mirror.einval.org/debian unstable/main arm64 libclone-perl arm64 0.46-1+b1 [13.6 kB] Get:36 http://mirror.einval.org/debian unstable/main arm64 libconfig-tiny-perl all 2.30-1 [18.9 kB] Get:37 http://mirror.einval.org/debian unstable/main arm64 libparams-util-perl arm64 1.102-2+b2 [23.8 kB] Get:38 http://mirror.einval.org/debian unstable/main arm64 libsub-install-perl all 0.929-1 [10.5 kB] Get:39 http://mirror.einval.org/debian unstable/main arm64 libdata-optlist-perl all 0.114-1 [10.6 kB] Get:40 http://mirror.einval.org/debian unstable/main arm64 libsub-exporter-perl all 0.990-1 [50.6 kB] Get:41 http://mirror.einval.org/debian unstable/main arm64 libconst-fast-perl all 0.014-2 [8792 B] Get:42 http://mirror.einval.org/debian unstable/main arm64 libcpanel-json-xs-perl arm64 4.37-1+b1 [127 kB] Get:43 http://mirror.einval.org/debian unstable/main arm64 libdevel-stacktrace-perl all 2.0500-1 [26.4 kB] Get:44 http://mirror.einval.org/debian unstable/main arm64 libexception-class-perl all 1.45-1 [34.6 kB] Get:45 http://mirror.einval.org/debian unstable/main arm64 libiterator-perl all 0.03+ds1-2 [18.8 kB] Get:46 http://mirror.einval.org/debian unstable/main arm64 libiterator-util-perl all 0.02+ds1-2 [14.0 kB] Get:47 http://mirror.einval.org/debian unstable/main arm64 libdata-dpath-perl all 0.59-1 [43.6 kB] Get:48 http://mirror.einval.org/debian unstable/main arm64 libdata-messagepack-perl arm64 1.02-1+b2 [31.2 kB] Get:49 http://mirror.einval.org/debian unstable/main arm64 libnet-domain-tld-perl all 1.75-3 [31.9 kB] Get:50 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-domain-perl all 0.10-1.1 [11.1 kB] Get:51 http://mirror.einval.org/debian unstable/main arm64 libnet-ipv6addr-perl all 1.02-1 [21.7 kB] Get:52 http://mirror.einval.org/debian unstable/main arm64 libnet-netmask-perl all 2.0002-2 [28.6 kB] Get:53 http://mirror.einval.org/debian unstable/main arm64 libnetaddr-ip-perl arm64 4.079+dfsg-2+b2 [97.7 kB] Get:54 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-ip-perl all 0.31-1 [20.6 kB] Get:55 http://mirror.einval.org/debian unstable/main arm64 libdata-validate-uri-perl all 0.07-2 [11.2 kB] Get:56 http://mirror.einval.org/debian unstable/main arm64 libdevel-size-perl arm64 0.83-2+b2 [24.1 kB] Get:57 http://mirror.einval.org/debian unstable/main arm64 libemail-address-xs-perl arm64 1.05-1+b2 [28.3 kB] Get:58 http://mirror.einval.org/debian unstable/main arm64 libencode-locale-perl all 1.05-3 [12.9 kB] Get:59 http://mirror.einval.org/debian unstable/main arm64 libipc-system-simple-perl all 1.30-2 [26.8 kB] Get:60 http://mirror.einval.org/debian unstable/main arm64 libfile-basedir-perl all 0.09-2 [15.1 kB] Get:61 http://mirror.einval.org/debian unstable/main arm64 libtimedate-perl all 2.3300-2 [39.3 kB] Get:62 http://mirror.einval.org/debian unstable/main arm64 libhttp-date-perl all 6.06-1 [10.7 kB] Get:63 http://mirror.einval.org/debian unstable/main arm64 libfile-listing-perl all 6.16-1 [12.4 kB] Get:64 http://mirror.einval.org/debian unstable/main arm64 libfont-ttf-perl all 1.06-2 [318 kB] Get:65 http://mirror.einval.org/debian unstable/main arm64 libio-html-perl all 1.004-3 [16.2 kB] Get:66 http://mirror.einval.org/debian unstable/main arm64 liblwp-mediatypes-perl all 6.04-2 [20.2 kB] Get:67 http://mirror.einval.org/debian unstable/main arm64 libhttp-message-perl all 6.45-1 [82.0 kB] Get:68 http://mirror.einval.org/debian unstable/main arm64 libhtml-form-perl all 6.11-1 [33.1 kB] Get:69 http://mirror.einval.org/debian unstable/main arm64 libhtml-html5-entities-perl all 0.004-3 [21.0 kB] Get:70 http://mirror.einval.org/debian unstable/main arm64 libhtml-tree-perl all 5.07-3 [211 kB] Get:71 http://mirror.einval.org/debian unstable/main arm64 libhttp-cookies-perl all 6.11-1 [19.1 kB] Get:72 http://mirror.einval.org/debian unstable/main arm64 libhttp-negotiate-perl all 6.01-2 [13.1 kB] Get:73 http://mirror.einval.org/debian unstable/main arm64 perl-openssl-defaults arm64 7+b1 [7924 B] Get:74 http://mirror.einval.org/debian unstable/main arm64 libnet-ssleay-perl arm64 1.94-1 [327 kB] Get:75 http://mirror.einval.org/debian unstable/main arm64 libio-socket-ssl-perl all 2.085-1 [218 kB] Get:76 http://mirror.einval.org/debian unstable/main arm64 libnet-http-perl all 6.23-1 [23.9 kB] Get:77 http://mirror.einval.org/debian unstable/main arm64 liblwp-protocol-https-perl all 6.13-1 [10.7 kB] Get:78 http://mirror.einval.org/debian unstable/main arm64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:79 http://mirror.einval.org/debian unstable/main arm64 libwww-perl all 6.76-1 [183 kB] Get:80 http://mirror.einval.org/debian unstable/main arm64 libhtml-tokeparser-simple-perl all 3.16-4 [39.1 kB] Get:81 http://mirror.einval.org/debian unstable/main arm64 libimport-into-perl all 1.002005-2 [11.3 kB] Get:82 http://mirror.einval.org/debian unstable/main arm64 libio-interactive-perl all 1.025-1 [11.4 kB] Get:83 http://mirror.einval.org/debian unstable/main arm64 libipc-run3-perl all 0.049-1 [31.5 kB] Get:84 http://mirror.einval.org/debian unstable/main arm64 libjson-maybexs-perl all 1.004005-1 [12.9 kB] Get:85 http://mirror.einval.org/debian unstable/main arm64 liblist-compare-perl all 0.55-2 [65.7 kB] Get:86 http://mirror.einval.org/debian unstable/main arm64 liblist-someutils-perl all 0.59-1 [37.1 kB] Get:87 http://mirror.einval.org/debian unstable/main arm64 liblist-utilsby-perl all 0.12-2 [15.5 kB] Get:88 http://mirror.einval.org/debian unstable/main arm64 liblz1 arm64 1.14-1 [37.7 kB] Get:89 http://mirror.einval.org/debian unstable/main arm64 liblzo2-2 arm64 2.10-2+b1 [49.2 kB] Get:90 http://mirror.einval.org/debian unstable/main arm64 libmarkdown2 arm64 2.2.7-2+b1 [33.2 kB] Get:91 http://mirror.einval.org/debian unstable/main arm64 libmldbm-perl all 2.05-4 [16.8 kB] Get:92 http://mirror.einval.org/debian unstable/main arm64 librole-tiny-perl all 2.002004-1 [21.4 kB] Get:93 http://mirror.einval.org/debian unstable/main arm64 libsub-quote-perl all 2.006008-1 [21.8 kB] Get:94 http://mirror.einval.org/debian unstable/main arm64 libmoo-perl all 2.005005-1 [58.0 kB] Get:95 http://mirror.einval.org/debian unstable/main arm64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:96 http://mirror.einval.org/debian unstable/main arm64 libmoox-aliases-perl all 0.001006-2 [7156 B] Get:97 http://mirror.einval.org/debian unstable/main arm64 libmouse-perl arm64 2.5.10-1+b4 [141 kB] Get:98 http://mirror.einval.org/debian unstable/main arm64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:99 http://mirror.einval.org/debian unstable/main arm64 libsub-identify-perl arm64 0.14-3+b1 [11.2 kB] Get:100 http://mirror.einval.org/debian unstable/main arm64 libsub-name-perl arm64 0.27-1+b1 [12.3 kB] Get:101 http://mirror.einval.org/debian unstable/main arm64 libnamespace-clean-perl all 0.27-2 [17.8 kB] Get:102 http://mirror.einval.org/debian unstable/main arm64 libpath-tiny-perl all 0.144-1 [56.4 kB] Get:103 http://mirror.einval.org/debian unstable/main arm64 libperlio-gzip-perl arm64 0.20-1+b2 [17.4 kB] Get:104 http://mirror.einval.org/debian unstable/main arm64 libperlio-utf8-strict-perl arm64 0.010-1+b1 [11.4 kB] Get:105 http://mirror.einval.org/debian unstable/main arm64 libproc-processtable-perl arm64 0.636-1+b1 [41.6 kB] Get:106 http://mirror.einval.org/debian unstable/main arm64 libregexp-wildcards-perl all 1.05-3 [14.1 kB] Get:107 http://mirror.einval.org/debian unstable/main arm64 libsereal-decoder-perl arm64 5.004+ds-1+b1 [95.7 kB] Get:108 http://mirror.einval.org/debian unstable/main arm64 libsereal-encoder-perl arm64 5.004+ds-1+b1 [97.7 kB] Get:109 http://mirror.einval.org/debian unstable/main arm64 libsort-versions-perl all 1.62-3 [8928 B] Get:110 http://mirror.einval.org/debian unstable/main arm64 libxs-parse-keyword-perl arm64 0.39-1+b1 [56.2 kB] Get:111 http://mirror.einval.org/debian unstable/main arm64 libsyntax-keyword-try-perl arm64 0.29-1+b1 [26.8 kB] Get:112 http://mirror.einval.org/debian unstable/main arm64 libterm-readkey-perl arm64 2.38-2+b2 [24.4 kB] Get:113 http://mirror.einval.org/debian unstable/main arm64 libtext-levenshteinxs-perl arm64 0.03-5+b2 [8656 B] Get:114 http://mirror.einval.org/debian unstable/main arm64 libtext-markdown-discount-perl arm64 0.16-1+b1 [13.1 kB] Get:115 http://mirror.einval.org/debian unstable/main arm64 libtext-xslate-perl arm64 3.5.9-1+b3 [171 kB] Get:116 http://mirror.einval.org/debian unstable/main arm64 libtime-duration-perl all 1.21-2 [13.1 kB] Get:117 http://mirror.einval.org/debian unstable/main arm64 libtime-moment-perl arm64 0.44-2+b2 [72.2 kB] Get:118 http://mirror.einval.org/debian unstable/main arm64 libunicode-utf8-perl arm64 0.62-2+b1 [19.9 kB] Get:119 http://mirror.einval.org/debian unstable/main arm64 libwww-mechanize-perl all 2.18-1 [114 kB] Get:120 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1 [50.4 kB] Get:121 http://mirror.einval.org/debian unstable/main arm64 libyaml-libyaml-perl arm64 0.89+ds-1 [33.0 kB] Get:122 http://mirror.einval.org/debian unstable/main arm64 plzip arm64 1.11-1 [58.8 kB] Get:123 http://mirror.einval.org/debian unstable/main arm64 lzop arm64 1.04-2 [82.8 kB] Get:124 http://mirror.einval.org/debian unstable/main arm64 patchutils arm64 0.4.2-1 [73.5 kB] Get:125 http://mirror.einval.org/debian unstable/main arm64 t1utils arm64 1.41-4 [59.8 kB] Get:126 http://mirror.einval.org/debian unstable/main arm64 unzip arm64 6.0-28 [157 kB] Get:127 http://mirror.einval.org/debian unstable/main arm64 lintian all 2.117.0 [1052 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 15.1 MB in 0s (55.6 MB/s) dpkg: libssl3:arm64: dependency problems, but removing anyway as you requested: libkrb5-3:arm64 depends on libssl3 (>= 3.0.0). coreutils depends on libssl3 (>= 3.0.0). (Reading database ... 18309 files and directories currently installed.) Removing libssl3:arm64 (3.1.5-1) ... Selecting previously unselected package libssl3t64:arm64. (Reading database ... 18296 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.1.5-1.1_arm64.deb ... Unpacking libssl3t64:arm64 (3.1.5-1.1) ... Setting up libssl3t64:arm64 (3.1.5-1.1) ... Selecting previously unselected package netbase. (Reading database ... 18311 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_8.2-3.1_all.deb ... Unpacking readline-common (8.2-3.1) ... Selecting previously unselected package openssl. Preparing to unpack .../002-openssl_3.1.5-1.1_arm64.deb ... Unpacking openssl (3.1.5-1.1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../003-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... Selecting previously unselected package diffstat. Preparing to unpack .../004-diffstat_1.65-1_arm64.deb ... Unpacking diffstat (1.65-1) ... Selecting previously unselected package libassuan0:arm64. Preparing to unpack .../005-libassuan0_2.5.6-1_arm64.deb ... Unpacking libassuan0:arm64 (2.5.6-1) ... Selecting previously unselected package libreadline8:arm64. Preparing to unpack .../006-libreadline8_8.2-3+b1_arm64.deb ... Unpacking libreadline8:arm64 (8.2-3+b1) ... Selecting previously unselected package gpgconf. Preparing to unpack .../007-gpgconf_2.2.40-1.1+b1_arm64.deb ... Unpacking gpgconf (2.2.40-1.1+b1) ... Selecting previously unselected package libsqlite3-0:arm64. Preparing to unpack .../008-libsqlite3-0_3.45.1-1_arm64.deb ... Unpacking libsqlite3-0:arm64 (3.45.1-1) ... Selecting previously unselected package gpg. Preparing to unpack .../009-gpg_2.2.40-1.1+b1_arm64.deb ... Unpacking gpg (2.2.40-1.1+b1) ... Selecting previously unselected package iso-codes. Preparing to unpack .../010-iso-codes_4.16.0-1_all.deb ... Unpacking iso-codes (4.16.0-1) ... Selecting previously unselected package libaliased-perl. Preparing to unpack .../011-libaliased-perl_0.34-3_all.deb ... Unpacking libaliased-perl (0.34-3) ... Selecting previously unselected package libapt-pkg-perl. Preparing to unpack .../012-libapt-pkg-perl_0.1.40+b4_arm64.deb ... Unpacking libapt-pkg-perl (0.1.40+b4) ... Selecting previously unselected package libb-hooks-op-check-perl:arm64. Preparing to unpack .../013-libb-hooks-op-check-perl_0.22-2+b2_arm64.deb ... Unpacking libb-hooks-op-check-perl:arm64 (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:arm64. Preparing to unpack .../015-libdevel-callchecker-perl_0.008-2+b1_arm64.deb ... Unpacking libdevel-callchecker-perl:arm64 (0.008-2+b1) ... Selecting previously unselected package libparams-classify-perl:arm64. Preparing to unpack .../016-libparams-classify-perl_0.015-2+b2_arm64.deb ... Unpacking libparams-classify-perl:arm64 (0.015-2+b2) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../017-libmodule-runtime-perl_0.016-2_all.deb ... Unpacking libmodule-runtime-perl (0.016-2) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../018-libtry-tiny-perl_0.31-2_all.deb ... Unpacking libtry-tiny-perl (0.31-2) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../019-libmodule-implementation-perl_0.09-2_all.deb ... Unpacking libmodule-implementation-perl (0.09-2) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../020-libsub-exporter-progressive-perl_0.001013-3_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001013-3) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../021-libvariable-magic-perl_0.63-1+b2_arm64.deb ... Unpacking libvariable-magic-perl (0.63-1+b2) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../022-libb-hooks-endofscope-perl_0.26-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.26-1) ... Selecting previously unselected package libberkeleydb-perl:arm64. Preparing to unpack .../023-libberkeleydb-perl_0.64-2+b2_arm64.deb ... Unpacking libberkeleydb-perl:arm64 (0.64-2+b2) ... Selecting previously unselected package libcapture-tiny-perl. Preparing to unpack .../024-libcapture-tiny-perl_0.48-2_all.deb ... Unpacking libcapture-tiny-perl (0.48-2) ... Selecting previously unselected package libhtml-tagset-perl. Preparing to unpack .../025-libhtml-tagset-perl_3.20-6_all.deb ... Unpacking libhtml-tagset-perl (3.20-6) ... Selecting previously unselected package liburi-perl. Preparing to unpack .../026-liburi-perl_5.27-1_all.deb ... Unpacking liburi-perl (5.27-1) ... Selecting previously unselected package libhtml-parser-perl:arm64. Preparing to unpack .../027-libhtml-parser-perl_3.81-1+b1_arm64.deb ... Unpacking libhtml-parser-perl:arm64 (3.81-1+b1) ... Selecting previously unselected package libcgi-pm-perl. Preparing to unpack .../028-libcgi-pm-perl_4.61-1_all.deb ... Unpacking libcgi-pm-perl (4.61-1) ... Selecting previously unselected package libclass-data-inheritable-perl. Preparing to unpack .../029-libclass-data-inheritable-perl_0.08-3_all.deb ... Unpacking libclass-data-inheritable-perl (0.08-3) ... Selecting previously unselected package libclass-method-modifiers-perl. Preparing to unpack .../030-libclass-method-modifiers-perl_2.15-1_all.deb ... Unpacking libclass-method-modifiers-perl (2.15-1) ... Selecting previously unselected package libclass-xsaccessor-perl. Preparing to unpack .../031-libclass-xsaccessor-perl_1.19-4+b2_arm64.deb ... Unpacking libclass-xsaccessor-perl (1.19-4+b2) ... Selecting previously unselected package libclone-perl:arm64. Preparing to unpack .../032-libclone-perl_0.46-1+b1_arm64.deb ... Unpacking libclone-perl:arm64 (0.46-1+b1) ... Selecting previously unselected package libconfig-tiny-perl. Preparing to unpack .../033-libconfig-tiny-perl_2.30-1_all.deb ... Unpacking libconfig-tiny-perl (2.30-1) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../034-libparams-util-perl_1.102-2+b2_arm64.deb ... Unpacking libparams-util-perl (1.102-2+b2) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../035-libsub-install-perl_0.929-1_all.deb ... Unpacking libsub-install-perl (0.929-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../036-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../037-libsub-exporter-perl_0.990-1_all.deb ... Unpacking libsub-exporter-perl (0.990-1) ... Selecting previously unselected package libconst-fast-perl. Preparing to unpack .../038-libconst-fast-perl_0.014-2_all.deb ... Unpacking libconst-fast-perl (0.014-2) ... Selecting previously unselected package libcpanel-json-xs-perl:arm64. Preparing to unpack .../039-libcpanel-json-xs-perl_4.37-1+b1_arm64.deb ... Unpacking libcpanel-json-xs-perl:arm64 (4.37-1+b1) ... Selecting previously unselected package libdevel-stacktrace-perl. Preparing to unpack .../040-libdevel-stacktrace-perl_2.0500-1_all.deb ... Unpacking libdevel-stacktrace-perl (2.0500-1) ... Selecting previously unselected package libexception-class-perl. Preparing to unpack .../041-libexception-class-perl_1.45-1_all.deb ... Unpacking libexception-class-perl (1.45-1) ... Selecting previously unselected package libiterator-perl. Preparing to unpack .../042-libiterator-perl_0.03+ds1-2_all.deb ... Unpacking libiterator-perl (0.03+ds1-2) ... Selecting previously unselected package libiterator-util-perl. Preparing to unpack .../043-libiterator-util-perl_0.02+ds1-2_all.deb ... Unpacking libiterator-util-perl (0.02+ds1-2) ... Selecting previously unselected package libdata-dpath-perl. Preparing to unpack .../044-libdata-dpath-perl_0.59-1_all.deb ... Unpacking libdata-dpath-perl (0.59-1) ... Selecting previously unselected package libdata-messagepack-perl. Preparing to unpack .../045-libdata-messagepack-perl_1.02-1+b2_arm64.deb ... Unpacking libdata-messagepack-perl (1.02-1+b2) ... Selecting previously unselected package libnet-domain-tld-perl. Preparing to unpack .../046-libnet-domain-tld-perl_1.75-3_all.deb ... Unpacking libnet-domain-tld-perl (1.75-3) ... Selecting previously unselected package libdata-validate-domain-perl. Preparing to unpack .../047-libdata-validate-domain-perl_0.10-1.1_all.deb ... Unpacking libdata-validate-domain-perl (0.10-1.1) ... Selecting previously unselected package libnet-ipv6addr-perl. Preparing to unpack .../048-libnet-ipv6addr-perl_1.02-1_all.deb ... Unpacking libnet-ipv6addr-perl (1.02-1) ... Selecting previously unselected package libnet-netmask-perl. Preparing to unpack .../049-libnet-netmask-perl_2.0002-2_all.deb ... Unpacking libnet-netmask-perl (2.0002-2) ... Selecting previously unselected package libnetaddr-ip-perl. Preparing to unpack .../050-libnetaddr-ip-perl_4.079+dfsg-2+b2_arm64.deb ... Unpacking libnetaddr-ip-perl (4.079+dfsg-2+b2) ... Selecting previously unselected package libdata-validate-ip-perl. Preparing to unpack .../051-libdata-validate-ip-perl_0.31-1_all.deb ... Unpacking libdata-validate-ip-perl (0.31-1) ... Selecting previously unselected package libdata-validate-uri-perl. Preparing to unpack .../052-libdata-validate-uri-perl_0.07-2_all.deb ... Unpacking libdata-validate-uri-perl (0.07-2) ... Selecting previously unselected package libdevel-size-perl. Preparing to unpack .../053-libdevel-size-perl_0.83-2+b2_arm64.deb ... Unpacking libdevel-size-perl (0.83-2+b2) ... Selecting previously unselected package libemail-address-xs-perl. Preparing to unpack .../054-libemail-address-xs-perl_1.05-1+b2_arm64.deb ... Unpacking libemail-address-xs-perl (1.05-1+b2) ... Selecting previously unselected package libencode-locale-perl. Preparing to unpack .../055-libencode-locale-perl_1.05-3_all.deb ... Unpacking libencode-locale-perl (1.05-3) ... Selecting previously unselected package libipc-system-simple-perl. Preparing to unpack .../056-libipc-system-simple-perl_1.30-2_all.deb ... Unpacking libipc-system-simple-perl (1.30-2) ... Selecting previously unselected package libfile-basedir-perl. Preparing to unpack .../057-libfile-basedir-perl_0.09-2_all.deb ... Unpacking libfile-basedir-perl (0.09-2) ... Selecting previously unselected package libtimedate-perl. Preparing to unpack .../058-libtimedate-perl_2.3300-2_all.deb ... Unpacking libtimedate-perl (2.3300-2) ... Selecting previously unselected package libhttp-date-perl. Preparing to unpack .../059-libhttp-date-perl_6.06-1_all.deb ... Unpacking libhttp-date-perl (6.06-1) ... Selecting previously unselected package libfile-listing-perl. Preparing to unpack .../060-libfile-listing-perl_6.16-1_all.deb ... Unpacking libfile-listing-perl (6.16-1) ... Selecting previously unselected package libfont-ttf-perl. Preparing to unpack .../061-libfont-ttf-perl_1.06-2_all.deb ... Unpacking libfont-ttf-perl (1.06-2) ... Selecting previously unselected package libio-html-perl. Preparing to unpack .../062-libio-html-perl_1.004-3_all.deb ... Unpacking libio-html-perl (1.004-3) ... Selecting previously unselected package liblwp-mediatypes-perl. Preparing to unpack .../063-liblwp-mediatypes-perl_6.04-2_all.deb ... Unpacking liblwp-mediatypes-perl (6.04-2) ... Selecting previously unselected package libhttp-message-perl. Preparing to unpack .../064-libhttp-message-perl_6.45-1_all.deb ... Unpacking libhttp-message-perl (6.45-1) ... Selecting previously unselected package libhtml-form-perl. Preparing to unpack .../065-libhtml-form-perl_6.11-1_all.deb ... Unpacking libhtml-form-perl (6.11-1) ... Selecting previously unselected package libhtml-html5-entities-perl. Preparing to unpack .../066-libhtml-html5-entities-perl_0.004-3_all.deb ... Unpacking libhtml-html5-entities-perl (0.004-3) ... Selecting previously unselected package libhtml-tree-perl. Preparing to unpack .../067-libhtml-tree-perl_5.07-3_all.deb ... Unpacking libhtml-tree-perl (5.07-3) ... Selecting previously unselected package libhttp-cookies-perl. Preparing to unpack .../068-libhttp-cookies-perl_6.11-1_all.deb ... Unpacking libhttp-cookies-perl (6.11-1) ... Selecting previously unselected package libhttp-negotiate-perl. Preparing to unpack .../069-libhttp-negotiate-perl_6.01-2_all.deb ... Unpacking libhttp-negotiate-perl (6.01-2) ... Selecting previously unselected package perl-openssl-defaults:arm64. Preparing to unpack .../070-perl-openssl-defaults_7+b1_arm64.deb ... Unpacking perl-openssl-defaults:arm64 (7+b1) ... Selecting previously unselected package libnet-ssleay-perl:arm64. Preparing to unpack .../071-libnet-ssleay-perl_1.94-1_arm64.deb ... Unpacking libnet-ssleay-perl:arm64 (1.94-1) ... Selecting previously unselected package libio-socket-ssl-perl. Preparing to unpack .../072-libio-socket-ssl-perl_2.085-1_all.deb ... Unpacking libio-socket-ssl-perl (2.085-1) ... Selecting previously unselected package libnet-http-perl. Preparing to unpack .../073-libnet-http-perl_6.23-1_all.deb ... Unpacking libnet-http-perl (6.23-1) ... Selecting previously unselected package liblwp-protocol-https-perl. Preparing to unpack .../074-liblwp-protocol-https-perl_6.13-1_all.deb ... Unpacking liblwp-protocol-https-perl (6.13-1) ... Selecting previously unselected package libwww-robotrules-perl. Preparing to unpack .../075-libwww-robotrules-perl_6.02-1_all.deb ... Unpacking libwww-robotrules-perl (6.02-1) ... Selecting previously unselected package libwww-perl. Preparing to unpack .../076-libwww-perl_6.76-1_all.deb ... Unpacking libwww-perl (6.76-1) ... Selecting previously unselected package libhtml-tokeparser-simple-perl. Preparing to unpack .../077-libhtml-tokeparser-simple-perl_3.16-4_all.deb ... Unpacking libhtml-tokeparser-simple-perl (3.16-4) ... Selecting previously unselected package libimport-into-perl. Preparing to unpack .../078-libimport-into-perl_1.002005-2_all.deb ... Unpacking libimport-into-perl (1.002005-2) ... Selecting previously unselected package libio-interactive-perl. Preparing to unpack .../079-libio-interactive-perl_1.025-1_all.deb ... Unpacking libio-interactive-perl (1.025-1) ... Selecting previously unselected package libipc-run3-perl. Preparing to unpack .../080-libipc-run3-perl_0.049-1_all.deb ... Unpacking libipc-run3-perl (0.049-1) ... Selecting previously unselected package libjson-maybexs-perl. Preparing to unpack .../081-libjson-maybexs-perl_1.004005-1_all.deb ... Unpacking libjson-maybexs-perl (1.004005-1) ... Selecting previously unselected package liblist-compare-perl. Preparing to unpack .../082-liblist-compare-perl_0.55-2_all.deb ... Unpacking liblist-compare-perl (0.55-2) ... Selecting previously unselected package liblist-someutils-perl. Preparing to unpack .../083-liblist-someutils-perl_0.59-1_all.deb ... Unpacking liblist-someutils-perl (0.59-1) ... Selecting previously unselected package liblist-utilsby-perl. Preparing to unpack .../084-liblist-utilsby-perl_0.12-2_all.deb ... Unpacking liblist-utilsby-perl (0.12-2) ... Selecting previously unselected package liblz1:arm64. Preparing to unpack .../085-liblz1_1.14-1_arm64.deb ... Unpacking liblz1:arm64 (1.14-1) ... Selecting previously unselected package liblzo2-2:arm64. Preparing to unpack .../086-liblzo2-2_2.10-2+b1_arm64.deb ... Unpacking liblzo2-2:arm64 (2.10-2+b1) ... Selecting previously unselected package libmarkdown2:arm64. Preparing to unpack .../087-libmarkdown2_2.2.7-2+b1_arm64.deb ... Unpacking libmarkdown2:arm64 (2.2.7-2+b1) ... Selecting previously unselected package libmldbm-perl. Preparing to unpack .../088-libmldbm-perl_2.05-4_all.deb ... Unpacking libmldbm-perl (2.05-4) ... Selecting previously unselected package librole-tiny-perl. Preparing to unpack .../089-librole-tiny-perl_2.002004-1_all.deb ... Unpacking librole-tiny-perl (2.002004-1) ... Selecting previously unselected package libsub-quote-perl. Preparing to unpack .../090-libsub-quote-perl_2.006008-1_all.deb ... Unpacking libsub-quote-perl (2.006008-1) ... Selecting previously unselected package libmoo-perl. Preparing to unpack .../091-libmoo-perl_2.005005-1_all.deb ... Unpacking libmoo-perl (2.005005-1) ... Selecting previously unselected package libstrictures-perl. Preparing to unpack .../092-libstrictures-perl_2.000006-1_all.deb ... Unpacking libstrictures-perl (2.000006-1) ... Selecting previously unselected package libmoox-aliases-perl. Preparing to unpack .../093-libmoox-aliases-perl_0.001006-2_all.deb ... Unpacking libmoox-aliases-perl (0.001006-2) ... Selecting previously unselected package libmouse-perl. Preparing to unpack .../094-libmouse-perl_2.5.10-1+b4_arm64.deb ... Unpacking libmouse-perl (2.5.10-1+b4) ... Selecting previously unselected package libpackage-stash-perl. Preparing to unpack .../095-libpackage-stash-perl_0.40-1_all.deb ... Unpacking libpackage-stash-perl (0.40-1) ... Selecting previously unselected package libsub-identify-perl. Preparing to unpack .../096-libsub-identify-perl_0.14-3+b1_arm64.deb ... Unpacking libsub-identify-perl (0.14-3+b1) ... Selecting previously unselected package libsub-name-perl:arm64. Preparing to unpack .../097-libsub-name-perl_0.27-1+b1_arm64.deb ... Unpacking libsub-name-perl:arm64 (0.27-1+b1) ... Selecting previously unselected package libnamespace-clean-perl. Preparing to unpack .../098-libnamespace-clean-perl_0.27-2_all.deb ... Unpacking libnamespace-clean-perl (0.27-2) ... Selecting previously unselected package libpath-tiny-perl. Preparing to unpack .../099-libpath-tiny-perl_0.144-1_all.deb ... Unpacking libpath-tiny-perl (0.144-1) ... Selecting previously unselected package libperlio-gzip-perl. Preparing to unpack .../100-libperlio-gzip-perl_0.20-1+b2_arm64.deb ... Unpacking libperlio-gzip-perl (0.20-1+b2) ... Selecting previously unselected package libperlio-utf8-strict-perl. Preparing to unpack .../101-libperlio-utf8-strict-perl_0.010-1+b1_arm64.deb ... Unpacking libperlio-utf8-strict-perl (0.010-1+b1) ... Selecting previously unselected package libproc-processtable-perl:arm64. Preparing to unpack .../102-libproc-processtable-perl_0.636-1+b1_arm64.deb ... Unpacking libproc-processtable-perl:arm64 (0.636-1+b1) ... Selecting previously unselected package libregexp-wildcards-perl. Preparing to unpack .../103-libregexp-wildcards-perl_1.05-3_all.deb ... Unpacking libregexp-wildcards-perl (1.05-3) ... Selecting previously unselected package libsereal-decoder-perl. Preparing to unpack .../104-libsereal-decoder-perl_5.004+ds-1+b1_arm64.deb ... Unpacking libsereal-decoder-perl (5.004+ds-1+b1) ... Selecting previously unselected package libsereal-encoder-perl. Preparing to unpack .../105-libsereal-encoder-perl_5.004+ds-1+b1_arm64.deb ... Unpacking libsereal-encoder-perl (5.004+ds-1+b1) ... Selecting previously unselected package libsort-versions-perl. Preparing to unpack .../106-libsort-versions-perl_1.62-3_all.deb ... Unpacking libsort-versions-perl (1.62-3) ... Selecting previously unselected package libxs-parse-keyword-perl. Preparing to unpack .../107-libxs-parse-keyword-perl_0.39-1+b1_arm64.deb ... Unpacking libxs-parse-keyword-perl (0.39-1+b1) ... Selecting previously unselected package libsyntax-keyword-try-perl. Preparing to unpack .../108-libsyntax-keyword-try-perl_0.29-1+b1_arm64.deb ... Unpacking libsyntax-keyword-try-perl (0.29-1+b1) ... Selecting previously unselected package libterm-readkey-perl. Preparing to unpack .../109-libterm-readkey-perl_2.38-2+b2_arm64.deb ... Unpacking libterm-readkey-perl (2.38-2+b2) ... Selecting previously unselected package libtext-levenshteinxs-perl. Preparing to unpack .../110-libtext-levenshteinxs-perl_0.03-5+b2_arm64.deb ... Unpacking libtext-levenshteinxs-perl (0.03-5+b2) ... Selecting previously unselected package libtext-markdown-discount-perl. Preparing to unpack .../111-libtext-markdown-discount-perl_0.16-1+b1_arm64.deb ... Unpacking libtext-markdown-discount-perl (0.16-1+b1) ... Selecting previously unselected package libtext-xslate-perl:arm64. Preparing to unpack .../112-libtext-xslate-perl_3.5.9-1+b3_arm64.deb ... Unpacking libtext-xslate-perl:arm64 (3.5.9-1+b3) ... Selecting previously unselected package libtime-duration-perl. Preparing to unpack .../113-libtime-duration-perl_1.21-2_all.deb ... Unpacking libtime-duration-perl (1.21-2) ... Selecting previously unselected package libtime-moment-perl. Preparing to unpack .../114-libtime-moment-perl_0.44-2+b2_arm64.deb ... Unpacking libtime-moment-perl (0.44-2+b2) ... Selecting previously unselected package libunicode-utf8-perl. Preparing to unpack .../115-libunicode-utf8-perl_0.62-2+b1_arm64.deb ... Unpacking libunicode-utf8-perl (0.62-2+b1) ... Selecting previously unselected package libwww-mechanize-perl. Preparing to unpack .../116-libwww-mechanize-perl_2.18-1_all.deb ... Unpacking libwww-mechanize-perl (2.18-1) ... Selecting previously unselected package libyaml-0-2:arm64. Preparing to unpack .../117-libyaml-0-2_0.2.5-1_arm64.deb ... Unpacking libyaml-0-2:arm64 (0.2.5-1) ... Selecting previously unselected package libyaml-libyaml-perl. Preparing to unpack .../118-libyaml-libyaml-perl_0.89+ds-1_arm64.deb ... Unpacking libyaml-libyaml-perl (0.89+ds-1) ... Selecting previously unselected package plzip. Preparing to unpack .../119-plzip_1.11-1_arm64.deb ... Unpacking plzip (1.11-1) ... Selecting previously unselected package lzop. Preparing to unpack .../120-lzop_1.04-2_arm64.deb ... Unpacking lzop (1.04-2) ... Selecting previously unselected package patchutils. Preparing to unpack .../121-patchutils_0.4.2-1_arm64.deb ... Unpacking patchutils (0.4.2-1) ... Selecting previously unselected package t1utils. Preparing to unpack .../122-t1utils_1.41-4_arm64.deb ... Unpacking t1utils (1.41-4) ... Selecting previously unselected package unzip. Preparing to unpack .../123-unzip_6.0-28_arm64.deb ... Unpacking unzip (6.0-28) ... Selecting previously unselected package lintian. Preparing to unpack .../124-lintian_2.117.0_all.deb ... Unpacking lintian (2.117.0) ... Selecting previously unselected package sbuild-build-depends-lintian-dummy:i386. Preparing to unpack .../125-sbuild-build-depends-lintian-dummy_0.invalid.0_i386.deb ... Unpacking sbuild-build-depends-lintian-dummy:i386 (0.invalid.0) ... Setting up libapt-pkg-perl (0.1.40+b4) ... Setting up liblz1:arm64 (1.14-1) ... Setting up libberkeleydb-perl:arm64 (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:arm64 (0.46-1+b1) ... Setting up libyaml-0-2:arm64 (0.2.5-1) ... Setting up libsub-identify-perl (0.14-3+b1) ... Setting up libcpanel-json-xs-perl:arm64 (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:arm64 (3.45.1-1) ... Setting up liblwp-mediatypes-perl (6.04-2) ... Setting up libyaml-libyaml-perl (0.89+ds-1) ... Setting up libio-interactive-perl (1.025-1) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up perl-openssl-defaults:arm64 (7+b1) ... Setting up libmldbm-perl (2.05-4) ... Setting up liblzo2-2:arm64 (2.10-2+b1) ... Setting up libtime-moment-perl (0.44-2+b2) ... Setting up libencode-locale-perl (1.05-3) ... Setting up libassuan0:arm64 (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:arm64 (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:arm64 (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:arm64 (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:arm64 (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 (3.1.5-1.1) ... Setting up libtext-levenshteinxs-perl (0.03-5+b2) ... Setting up libperlio-gzip-perl (0.20-1+b2) ... Setting up readline-common (8.2-3.1) ... Setting up libhtml-html5-entities-perl (0.004-3) ... Setting up libsereal-decoder-perl (5.004+ds-1+b1) ... Setting up libmarkdown2:arm64 (2.2.7-2+b1) ... Setting up liburi-perl (5.27-1) ... 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:arm64 (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:arm64 (8.2-3+b1) ... 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:arm64 (0.008-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 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:arm64 (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:arm64 (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 (2.18-1) ... Setting up liblwp-protocol-https-perl (6.13-1) ... Setting up lintian (2.117.0) ... Setting up sbuild-build-depends-lintian-dummy:i386 (0.invalid.0) ... Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for man-db (2.12.0-3) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for ca-certificates (20240203) ... 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: arm64 Build Profiles: cross nocheck Build Type: any Build-Space: 363008 Build-Time: 1457 Distribution: unstable Foreign Architectures: i386 Host Architecture: i386 Install-Time: 48 Job: fastml_3.11-4 Lintian: pass Machine Architecture: arm64 Package: fastml Package-Time: 1567 Source-Version: 3.11-4 Space: 363008 Status: successful Version: 3.11-4 -------------------------------------------------------------------------------- Finished at 2024-03-01T20:20:34Z Build needed 00:26:07, 363008k disk space