https://launchpad.net/ubuntu/+archive/test-rebuild-20240502-noble/+build/28173734
RUN: /usr/share/launchpad-buildd/bin/builder-prep 
Kernel version: Linux bos03-riscv64-015 6.5.0-28-generic #29.1~22.04.1-Ubuntu SMP Wed Apr 10 02:20:48 UTC 2024 riscv64
Buildd toolchain package versions: launchpad-buildd_237~660~ubuntu22.04.1 python3-lpbuildd_237~660~ubuntu22.04.1 sbuild_0.81.2ubuntu6 git-build-recipe_0.3.6 git_1:2.34.1-1ubuntu1.10 dpkg-dev_1.21.1ubuntu2.3 python3-debian_0.1.43ubuntu1.1.
Syncing the system clock with the buildd NTP service...
10 May 19:31:59 ntpdate[2230]: adjust time server 10.211.37.1 offset -0.001486 sec
RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28173734 --image-type chroot /home/buildd/filecache-default/20a3246b7a16d5658607d7f37229fcda30a33651
Creating target for build PACKAGEBUILD-28173734
RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28173734
Starting target for build PACKAGEBUILD-28173734
RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28173734 'deb http://ftpmaster.internal/ubuntu noble main universe'
Overriding sources.list in build-PACKAGEBUILD-28173734
RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28173734
Updating target for build PACKAGEBUILD-28173734
Get:1 http://ftpmaster.internal/ubuntu noble InRelease [256 kB]
Get:2 http://ftpmaster.internal/ubuntu noble/main riscv64 Packages [1318 kB]
Get:3 http://ftpmaster.internal/ubuntu noble/main Translation-en [513 kB]
Get:4 http://ftpmaster.internal/ubuntu noble/universe riscv64 Packages [14.3 MB]
Get:5 http://ftpmaster.internal/ubuntu noble/universe Translation-en [5982 kB]
Fetched 22.4 MB in 32s (707 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:
  libnsl-dev libperl5.36 libtirpc-dev libunistring2 perl-modules-5.36
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
  libapt-pkg6.0* libdb5.3* libext2fs2* libgdbm-compat4* libgdbm6* libgnutls30*
  libhogweed6* libnettle8* libnpth0* libpng16-16* libreadline8* libssl3*
  libtirpc3* usrmerge*
The following NEW packages will be installed:
  cpp-13-riscv64-linux-gnu cpp-riscv64-linux-gnu g++-13-riscv64-linux-gnu
  g++-riscv64-linux-gnu gcc-13-riscv64-linux-gnu gcc-14-base
  gcc-riscv64-linux-gnu libapt-pkg6.0t64 libdb5.3t64 libext2fs2t64
  libgdbm-compat4t64 libgdbm6t64 libgnutls30t64 libhogweed6t64 libnettle8t64
  libnpth0t64 libperl5.38t64 libpng16-16t64 libreadline8t64 libssl3t64
  libtirpc3t64 libubsan1 libunistring5 perl-modules-5.38
The following packages will be upgraded:
  advancecomp apt apt-utils base-files base-passwd bash bash-completion
  binutils binutils-common binutils-riscv64-linux-gnu bsdextrautils bsdutils
  bzip2 ca-certificates coreutils cpp cpp-13 dash debconf debconf-i18n
  debianutils diffutils dpkg dpkg-dev e2fsprogs fakeroot findutils g++ g++-13
  gcc gcc-13 gcc-13-base gpg gpg-agent gpgconf gpgv grep gzip hostname init
  init-system-helpers krb5-locales libacl1 libapparmor1 libargon2-1 libasan8
  libassuan0 libatomic1 libattr1 libaudit-common libaudit1 libbinutils
  libblkid1 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0
  libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12
  libctf-nobfd0 libctf0 libdebconfclient0 libdevmapper1.02.1 libdpkg-perl
  libfakeroot libfdisk1 libffi8 libgcc-13-dev libgcc-s1 libgcrypt20 libgmp10
  libgomp1 libgpg-error-l10n libgpg-error0 libgpm2 libgssapi-krb5-2 libidn2-0
  libip4tc2 libisl23 libjansson4 libjson-c5 libk5crypto3 libkeyutils1 libkmod2
  libkrb5-3 libkrb5support0 liblocale-gettext-perl liblockfile-bin
  liblockfile1 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6
  libncursesw6 libnsl-dev libnsl2 libnss-nis libnss-nisplus libp11-kit0
  libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0
  libproc2-0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2
  libsframe1 libsmartcols1 libsqlite3-0 libss2 libstdc++-13-dev libstdc++6
  libsystemd-shared libsystemd0 libtasn1-6 libtext-charwidth-perl
  libtext-iconv-perl libtinfo6 libtirpc-common libtirpc-dev libudev1 libuuid1
  libxxhash0 libzstd1 linux-libc-dev lockfile-progs login logsave
  lto-disabled-list make mawk mount ncurses-base ncurses-bin openssl optipng
  passwd patch perl perl-base pinentry-curses procps psmisc readline-common
  rpcsvc-proto sed sensible-utils systemd systemd-dev systemd-sysv
  sysvinit-utils tar tzdata ubuntu-keyring util-linux uuid-runtime xz-utils
  zlib1g
170 upgraded, 24 newly installed, 14 to remove and 0 not upgraded.
Need to get 115 MB of archives.
After this operation, 71.2 MB of additional disk space will be used.
Get:1 http://ftpmaster.internal/ubuntu noble/main riscv64 libtirpc-common all 1.3.4+ds-1.1build1 [8094 B]
Get:2 http://ftpmaster.internal/ubuntu noble/main riscv64 libtirpc-dev riscv64 1.3.4+ds-1.1build1 [350 kB]
Get:3 http://ftpmaster.internal/ubuntu noble/main riscv64 libnsl-dev riscv64 1.3.0-3build3 [137 kB]
Get:4 http://ftpmaster.internal/ubuntu noble/main riscv64 libnsl2 riscv64 1.3.0-3build3 [43.3 kB]
Get:5 http://ftpmaster.internal/ubuntu noble/main riscv64 libtirpc3t64 riscv64 1.3.4+ds-1.1build1 [92.3 kB]
Get:6 http://ftpmaster.internal/ubuntu noble/main riscv64 libgssapi-krb5-2 riscv64 1.20.1-6ubuntu2 [153 kB]
Get:7 http://ftpmaster.internal/ubuntu noble/main riscv64 libkrb5-3 riscv64 1.20.1-6ubuntu2 [385 kB]
Get:8 http://ftpmaster.internal/ubuntu noble/main riscv64 libk5crypto3 riscv64 1.20.1-6ubuntu2 [108 kB]
Get:9 http://ftpmaster.internal/ubuntu noble/main riscv64 libkrb5support0 riscv64 1.20.1-6ubuntu2 [36.7 kB]
Get:10 http://ftpmaster.internal/ubuntu noble/main riscv64 libacl1 riscv64 2.3.2-1build1 [18.7 kB]
Get:11 http://ftpmaster.internal/ubuntu noble/main riscv64 libapparmor1 riscv64 4.0.0-beta3-0ubuntu3 [51.2 kB]
Get:12 http://ftpmaster.internal/ubuntu noble/main riscv64 libaudit-common all 1:3.1.2-2.1build1 [5736 B]
Get:13 http://ftpmaster.internal/ubuntu noble/main riscv64 libcap-ng0 riscv64 0.8.4-2build2 [15.5 kB]
Get:14 http://ftpmaster.internal/ubuntu noble/main riscv64 libaudit1 riscv64 1:3.1.2-2.1build1 [47.9 kB]
Get:15 http://ftpmaster.internal/ubuntu noble/main riscv64 libblkid1 riscv64 2.39.3-9ubuntu6 [204 kB]
Get:16 http://ftpmaster.internal/ubuntu noble/main riscv64 libcap2 riscv64 1:2.66-5ubuntu2 [31.8 kB]
Get:17 http://ftpmaster.internal/ubuntu noble/main riscv64 libcrypt-dev riscv64 1:4.4.36-4build1 [250 kB]
Get:18 http://ftpmaster.internal/ubuntu noble/main riscv64 libcrypt1 riscv64 1:4.4.36-4build1 [102 kB]
Get:19 http://ftpmaster.internal/ubuntu noble/main riscv64 libgpg-error-l10n all 1.47-3build2 [8064 B]
Get:20 http://ftpmaster.internal/ubuntu noble/main riscv64 libgpg-error0 riscv64 1.47-3build2 [75.8 kB]
Get:21 http://ftpmaster.internal/ubuntu noble/main riscv64 libgcrypt20 riscv64 1.10.3-2build1 [564 kB]
Get:22 http://ftpmaster.internal/ubuntu noble/main riscv64 liblzma5 riscv64 5.6.1+really5.4.5-1 [130 kB]
Get:23 http://ftpmaster.internal/ubuntu noble/main riscv64 libzstd1 riscv64 1.5.5+dfsg2-2build1 [353 kB]
Get:24 http://ftpmaster.internal/ubuntu noble/main riscv64 libkmod2 riscv64 31+20240202-2ubuntu7 [55.1 kB]
Get:25 http://ftpmaster.internal/ubuntu noble/main riscv64 liblz4-1 riscv64 1.9.4-1build1 [85.7 kB]
Get:26 http://ftpmaster.internal/ubuntu noble/main riscv64 libpcre2-8-0 riscv64 10.42-4ubuntu2 [152 kB]
Get:27 http://ftpmaster.internal/ubuntu noble/main riscv64 libselinux1 riscv64 3.5-2ubuntu2 [86.1 kB]
Get:28 http://ftpmaster.internal/ubuntu noble/main riscv64 libmount1 riscv64 2.39.3-9ubuntu6 [212 kB]
Get:29 http://ftpmaster.internal/ubuntu noble/main riscv64 perl-modules-5.38 all 5.38.2-3.2build2 [3110 kB]
Get:30 http://ftpmaster.internal/ubuntu noble/main riscv64 libdb5.3t64 riscv64 5.3.28+dfsg2-7 [779 kB]
Get:31 http://ftpmaster.internal/ubuntu noble/main riscv64 libgdbm6t64 riscv64 1.23-5.1build1 [35.9 kB]
Get:32 http://ftpmaster.internal/ubuntu noble/main riscv64 libgdbm-compat4t64 riscv64 1.23-5.1build1 [6884 B]
Get:33 http://ftpmaster.internal/ubuntu noble/main riscv64 libperl5.38t64 riscv64 5.38.2-3.2build2 [4469 kB]
Get:34 http://ftpmaster.internal/ubuntu noble/main riscv64 perl riscv64 5.38.2-3.2build2 [231 kB]
Get:35 http://ftpmaster.internal/ubuntu noble/main riscv64 perl-base riscv64 5.38.2-3.2build2 [1834 kB]
Get:36 http://ftpmaster.internal/ubuntu noble/main riscv64 liblocale-gettext-perl riscv64 1.07-6ubuntu5 [15.7 kB]
Get:37 http://ftpmaster.internal/ubuntu noble/main riscv64 libtext-iconv-perl riscv64 1.7-8build3 [13.5 kB]
Get:38 http://ftpmaster.internal/ubuntu noble/main riscv64 libtext-charwidth-perl riscv64 0.04-11build3 [9272 B]
Get:39 http://ftpmaster.internal/ubuntu noble/main riscv64 openssl riscv64 3.0.13-0ubuntu3 [992 kB]
Get:40 http://ftpmaster.internal/ubuntu noble/main riscv64 libsystemd-shared riscv64 255.4-1ubuntu8 [2181 kB]
Get:41 http://ftpmaster.internal/ubuntu noble/main riscv64 libcryptsetup12 riscv64 2:2.7.0-1ubuntu4 [274 kB]
Get:42 http://ftpmaster.internal/ubuntu noble/main riscv64 libssl3t64 riscv64 3.0.13-0ubuntu3 [1735 kB]
Get:43 http://ftpmaster.internal/ubuntu noble/main riscv64 systemd-dev all 255.4-1ubuntu8 [104 kB]
Get:44 http://ftpmaster.internal/ubuntu noble/main riscv64 systemd-sysv riscv64 255.4-1ubuntu8 [11.9 kB]
Get:45 http://ftpmaster.internal/ubuntu noble/main riscv64 systemd riscv64 255.4-1ubuntu8 [3553 kB]
Get:46 http://ftpmaster.internal/ubuntu noble/main riscv64 libsystemd0 riscv64 255.4-1ubuntu8 [458 kB]
Get:47 http://ftpmaster.internal/ubuntu noble/main riscv64 libpam-modules-bin riscv64 1.5.3-5ubuntu5 [55.0 kB]
Get:48 http://ftpmaster.internal/ubuntu noble/main riscv64 libpam-modules riscv64 1.5.3-5ubuntu5 [284 kB]
Get:49 http://ftpmaster.internal/ubuntu noble/main riscv64 libnettle8t64 riscv64 3.9.1-2.2build1 [217 kB]
Get:50 http://ftpmaster.internal/ubuntu noble/main riscv64 libhogweed6t64 riscv64 3.9.1-2.2build1 [200 kB]
Get:51 http://ftpmaster.internal/ubuntu noble/main riscv64 libp11-kit0 riscv64 0.25.3-4ubuntu2 [318 kB]
Get:52 http://ftpmaster.internal/ubuntu noble/main riscv64 libunistring5 riscv64 1.1-2build1 [542 kB]
Get:53 http://ftpmaster.internal/ubuntu noble/main riscv64 libgnutls30t64 riscv64 3.8.3-1.1ubuntu3 [1012 kB]
Get:54 http://ftpmaster.internal/ubuntu noble/main riscv64 libapt-pkg6.0t64 riscv64 2.7.14build2 [1050 kB]
Get:55 http://ftpmaster.internal/ubuntu noble/main riscv64 bzip2 riscv64 1.0.8-5.1 [35.0 kB]
Get:56 http://ftpmaster.internal/ubuntu noble/main riscv64 libbz2-1.0 riscv64 1.0.8-5.1 [40.2 kB]
Get:57 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc-14-base riscv64 14-20240412-0ubuntu1 [47.6 kB]
Get:58 http://ftpmaster.internal/ubuntu noble/main riscv64 libgcc-s1 riscv64 14-20240412-0ubuntu1 [61.1 kB]
Get:59 http://ftpmaster.internal/ubuntu noble/main riscv64 libstdc++6 riscv64 14-20240412-0ubuntu1 [806 kB]
Get:60 http://ftpmaster.internal/ubuntu noble/main riscv64 libudev1 riscv64 255.4-1ubuntu8 [181 kB]
Get:61 http://ftpmaster.internal/ubuntu noble/main riscv64 libxxhash0 riscv64 0.8.2-2build1 [45.5 kB]
Get:62 http://ftpmaster.internal/ubuntu noble/main riscv64 zlib1g riscv64 1:1.3.dfsg-3.1ubuntu2 [60.8 kB]
Get:63 http://ftpmaster.internal/ubuntu noble/main riscv64 libgmp10 riscv64 2:6.3.0+dfsg-2ubuntu6 [258 kB]
Get:64 http://ftpmaster.internal/ubuntu noble/main riscv64 libffi8 riscv64 3.4.6-1build1 [23.1 kB]
Get:65 http://ftpmaster.internal/ubuntu noble/main riscv64 libidn2-0 riscv64 2.3.7-2build1 [102 kB]
Get:66 http://ftpmaster.internal/ubuntu noble/main riscv64 libtasn1-6 riscv64 4.19.0-3build1 [45.3 kB]
Get:67 http://ftpmaster.internal/ubuntu noble/main riscv64 libdebconfclient0 riscv64 0.271ubuntu3 [11.2 kB]
Get:68 http://ftpmaster.internal/ubuntu noble/main riscv64 base-passwd riscv64 3.6.3build1 [52.7 kB]
Get:69 http://ftpmaster.internal/ubuntu noble/main riscv64 libassuan0 riscv64 2.5.6-1build1 [39.4 kB]
Get:70 http://ftpmaster.internal/ubuntu noble/main riscv64 libsqlite3-0 riscv64 3.45.1-1ubuntu2 [739 kB]
Get:71 http://ftpmaster.internal/ubuntu noble/main riscv64 gpg riscv64 2.4.4-2ubuntu17 [607 kB]
Get:72 http://ftpmaster.internal/ubuntu noble/main riscv64 libreadline8t64 riscv64 8.2-4build1 [156 kB]
Get:73 http://ftpmaster.internal/ubuntu noble/main riscv64 readline-common all 8.2-4build1 [56.5 kB]
Get:74 http://ftpmaster.internal/ubuntu noble/main riscv64 libncursesw6 riscv64 6.4+20240113-1ubuntu2 [155 kB]
Get:75 http://ftpmaster.internal/ubuntu noble/main riscv64 libtinfo6 riscv64 6.4+20240113-1ubuntu2 [109 kB]
Get:76 http://ftpmaster.internal/ubuntu noble/main riscv64 gpg-agent riscv64 2.4.4-2ubuntu17 [282 kB]
Get:77 http://ftpmaster.internal/ubuntu noble/main riscv64 gpgconf riscv64 2.4.4-2ubuntu17 [133 kB]
Get:78 http://ftpmaster.internal/ubuntu noble/main riscv64 pinentry-curses riscv64 1.2.1-3ubuntu5 [40.6 kB]
Get:79 http://ftpmaster.internal/ubuntu noble/main riscv64 init-system-helpers all 1.66ubuntu1 [39.4 kB]
Get:80 http://ftpmaster.internal/ubuntu noble/main riscv64 libnpth0t64 riscv64 1.6-3.1build1 [8144 B]
Get:81 http://ftpmaster.internal/ubuntu noble/main riscv64 gpgv riscv64 2.4.4-2ubuntu17 [276 kB]
Get:82 http://ftpmaster.internal/ubuntu noble/main riscv64 ubuntu-keyring all 2023.11.28.1 [11.1 kB]
Get:83 http://ftpmaster.internal/ubuntu noble/main riscv64 apt-utils riscv64 2.7.14build2 [226 kB]
Get:84 http://ftpmaster.internal/ubuntu noble/main riscv64 apt riscv64 2.7.14build2 [1349 kB]
Get:85 http://ftpmaster.internal/ubuntu noble/main riscv64 debconf-i18n all 1.5.86ubuntu1 [205 kB]
Get:86 http://ftpmaster.internal/ubuntu noble/main riscv64 debconf all 1.5.86ubuntu1 [124 kB]
Get:87 http://ftpmaster.internal/ubuntu noble/main riscv64 libpam0g riscv64 1.5.3-5ubuntu5 [69.1 kB]
Get:88 http://ftpmaster.internal/ubuntu noble/main riscv64 libseccomp2 riscv64 2.5.5-1ubuntu3 [52.9 kB]
Get:89 http://ftpmaster.internal/ubuntu noble/main riscv64 libargon2-1 riscv64 0~20190702+dfsg-4build1 [25.0 kB]
Get:90 http://ftpmaster.internal/ubuntu noble/main riscv64 libdevmapper1.02.1 riscv64 2:1.02.185-3ubuntu3 [145 kB]
Get:91 http://ftpmaster.internal/ubuntu noble/main riscv64 libjson-c5 riscv64 0.17-1build1 [37.4 kB]
Get:92 http://ftpmaster.internal/ubuntu noble/main riscv64 libuuid1 riscv64 2.39.3-9ubuntu6 [37.7 kB]
Get:93 http://ftpmaster.internal/ubuntu noble/main riscv64 libfdisk1 riscv64 2.39.3-9ubuntu6 [238 kB]
Get:94 http://ftpmaster.internal/ubuntu noble/main riscv64 mount riscv64 2.39.3-9ubuntu6 [152 kB]
Get:95 http://ftpmaster.internal/ubuntu noble/main riscv64 libcom-err2 riscv64 1.47.0-2.4~exp1ubuntu4 [22.5 kB]
Get:96 http://ftpmaster.internal/ubuntu noble/main riscv64 libkeyutils1 riscv64 1.6.3-3build1 [9804 B]
Get:97 http://ftpmaster.internal/ubuntu noble/universe riscv64 libnss-nisplus riscv64 1.3-5build1 [23.8 kB]
Get:98 http://ftpmaster.internal/ubuntu noble/universe riscv64 libnss-nis riscv64 3.1-0ubuntu7 [28.1 kB]
Get:99 http://ftpmaster.internal/ubuntu noble/main riscv64 rpcsvc-proto riscv64 1.4.2-0ubuntu7 [65.8 kB]
Get:100 http://ftpmaster.internal/ubuntu noble/main riscv64 libc6-dev riscv64 2.39-0ubuntu8 [3458 kB]
Get:101 http://ftpmaster.internal/ubuntu noble/main riscv64 libc-dev-bin riscv64 2.39-0ubuntu8 [20.0 kB]
Get:102 http://ftpmaster.internal/ubuntu noble/main riscv64 linux-libc-dev riscv64 6.8.0-31.31 [1568 kB]
Get:103 http://ftpmaster.internal/ubuntu noble/main riscv64 libc6 riscv64 2.39-0ubuntu8 [2776 kB]
Get:104 http://ftpmaster.internal/ubuntu noble/main riscv64 libc-bin riscv64 2.39-0ubuntu8 [609 kB]
Get:105 http://ftpmaster.internal/ubuntu noble/main riscv64 base-files riscv64 13ubuntu10 [73.5 kB]
Get:106 http://ftpmaster.internal/ubuntu noble/main riscv64 debianutils riscv64 5.17build1 [89.8 kB]
Get:107 http://ftpmaster.internal/ubuntu noble/main riscv64 bash riscv64 5.2.21-2ubuntu4 [745 kB]
Get:108 http://ftpmaster.internal/ubuntu noble/main riscv64 bsdutils riscv64 1:2.39.3-9ubuntu6 [116 kB]
Get:109 http://ftpmaster.internal/ubuntu noble/main riscv64 coreutils riscv64 9.4-3ubuntu6 [1459 kB]
Get:110 http://ftpmaster.internal/ubuntu noble/main riscv64 tar riscv64 1.35+dfsg-3build1 [269 kB]
Get:111 http://ftpmaster.internal/ubuntu noble/main riscv64 dpkg riscv64 1.22.6ubuntu6 [1285 kB]
Get:112 http://ftpmaster.internal/ubuntu noble/main riscv64 dash riscv64 0.5.12-6ubuntu5 [93.2 kB]
Get:113 http://ftpmaster.internal/ubuntu noble/main riscv64 diffutils riscv64 1:3.10-1build1 [184 kB]
Get:114 http://ftpmaster.internal/ubuntu noble/main riscv64 findutils riscv64 4.9.0-5build1 [315 kB]
Get:115 http://ftpmaster.internal/ubuntu noble/main riscv64 grep riscv64 3.11-4build1 [169 kB]
Get:116 http://ftpmaster.internal/ubuntu noble/main riscv64 gzip riscv64 1.12-1ubuntu3 [102 kB]
Get:117 http://ftpmaster.internal/ubuntu noble/main riscv64 hostname riscv64 3.23+nmu2ubuntu2 [11.4 kB]
Get:118 http://ftpmaster.internal/ubuntu noble/main riscv64 login riscv64 1:4.13+dfsg1-4ubuntu3 [204 kB]
Get:119 http://ftpmaster.internal/ubuntu noble/main riscv64 ncurses-bin riscv64 6.4+20240113-1ubuntu2 [187 kB]
Get:120 http://ftpmaster.internal/ubuntu noble/main riscv64 sed riscv64 4.9-2build1 [200 kB]
Get:121 http://ftpmaster.internal/ubuntu noble/main riscv64 util-linux riscv64 2.39.3-9ubuntu6 [1330 kB]
Get:122 http://ftpmaster.internal/ubuntu noble/main riscv64 ncurses-base all 6.4+20240113-1ubuntu2 [25.5 kB]
Get:123 http://ftpmaster.internal/ubuntu noble/main riscv64 sysvinit-utils riscv64 3.08-6ubuntu3 [35.1 kB]
Get:124 http://ftpmaster.internal/ubuntu noble/main riscv64 logsave riscv64 1.47.0-2.4~exp1ubuntu4 [22.3 kB]
Get:125 http://ftpmaster.internal/ubuntu noble/main riscv64 libext2fs2t64 riscv64 1.47.0-2.4~exp1ubuntu4 [243 kB]
Get:126 http://ftpmaster.internal/ubuntu noble/main riscv64 e2fsprogs riscv64 1.47.0-2.4~exp1ubuntu4 [604 kB]
Get:127 http://ftpmaster.internal/ubuntu noble/main riscv64 optipng riscv64 0.7.8+ds-1build2 [115 kB]
Get:128 http://ftpmaster.internal/ubuntu noble/main riscv64 libpng16-16t64 riscv64 1.6.43-5build1 [193 kB]
Get:129 http://ftpmaster.internal/ubuntu noble/main riscv64 init riscv64 1.66ubuntu1 [6190 B]
Get:130 http://ftpmaster.internal/ubuntu noble/main riscv64 libsmartcols1 riscv64 2.39.3-9ubuntu6 [146 kB]
Get:131 http://ftpmaster.internal/ubuntu noble/main riscv64 uuid-runtime riscv64 2.39.3-9ubuntu6 [49.2 kB]
Get:132 http://ftpmaster.internal/ubuntu noble/main riscv64 libattr1 riscv64 1:2.5.2-1build1 [11.4 kB]
Get:133 http://ftpmaster.internal/ubuntu noble/main riscv64 libmd0 riscv64 1.1.0-2build1 [30.5 kB]
Get:134 http://ftpmaster.internal/ubuntu noble/main riscv64 libpam-runtime all 1.5.3-5ubuntu5 [40.8 kB]
Get:135 http://ftpmaster.internal/ubuntu noble/main riscv64 libsemanage-common all 3.5-1build5 [10.1 kB]
Get:136 http://ftpmaster.internal/ubuntu noble/main riscv64 libsepol2 riscv64 3.5-2build1 [319 kB]
Get:137 http://ftpmaster.internal/ubuntu noble/main riscv64 libsemanage2 riscv64 3.5-1build5 [101 kB]
Get:138 http://ftpmaster.internal/ubuntu noble/main riscv64 passwd riscv64 1:4.13+dfsg1-4ubuntu3 [864 kB]
Get:139 http://ftpmaster.internal/ubuntu noble/main riscv64 libproc2-0 riscv64 2:4.0.4-4ubuntu3 [60.9 kB]
Get:140 http://ftpmaster.internal/ubuntu noble/main riscv64 libss2 riscv64 1.47.0-2.4~exp1ubuntu4 [17.1 kB]
Get:141 http://ftpmaster.internal/ubuntu noble/main riscv64 mawk riscv64 1.3.4.20240123-1build1 [129 kB]
Get:142 http://ftpmaster.internal/ubuntu noble/main riscv64 procps riscv64 2:4.0.4-4ubuntu3 [715 kB]
Get:143 http://ftpmaster.internal/ubuntu noble/main riscv64 sensible-utils all 0.0.22 [22.5 kB]
Get:144 http://ftpmaster.internal/ubuntu noble/main riscv64 ca-certificates all 20240203 [159 kB]
Get:145 http://ftpmaster.internal/ubuntu noble/main riscv64 krb5-locales all 1.20.1-6ubuntu2 [13.8 kB]
Get:146 http://ftpmaster.internal/ubuntu noble/main riscv64 tzdata all 2024a-2ubuntu1 [273 kB]
Get:147 http://ftpmaster.internal/ubuntu noble/main riscv64 bash-completion all 1:2.11-8 [180 kB]
Get:148 http://ftpmaster.internal/ubuntu noble/main riscv64 bsdextrautils riscv64 2.39.3-9ubuntu6 [92.2 kB]
Get:149 http://ftpmaster.internal/ubuntu noble/main riscv64 libgpm2 riscv64 1.20.7-11 [15.0 kB]
Get:150 http://ftpmaster.internal/ubuntu noble/main riscv64 libip4tc2 riscv64 1.8.10-3ubuntu2 [23.9 kB]
Get:151 http://ftpmaster.internal/ubuntu noble/main riscv64 libjansson4 riscv64 2.14-2build2 [34.7 kB]
Get:152 http://ftpmaster.internal/ubuntu noble/main riscv64 psmisc riscv64 23.7-1build1 [177 kB]
Get:153 http://ftpmaster.internal/ubuntu noble/main riscv64 xz-utils riscv64 5.6.1+really5.4.5-1 [269 kB]
Get:154 http://ftpmaster.internal/ubuntu noble/main riscv64 advancecomp riscv64 2.5-1build1 [237 kB]
Get:155 http://ftpmaster.internal/ubuntu noble/main riscv64 libctf0 riscv64 2.42-4ubuntu2 [104 kB]
Get:156 http://ftpmaster.internal/ubuntu noble/main riscv64 libctf-nobfd0 riscv64 2.42-4ubuntu2 [106 kB]
Get:157 http://ftpmaster.internal/ubuntu noble/main riscv64 binutils-riscv64-linux-gnu riscv64 2.42-4ubuntu2 [899 kB]
Get:158 http://ftpmaster.internal/ubuntu noble/main riscv64 libbinutils riscv64 2.42-4ubuntu2 [566 kB]
Get:159 http://ftpmaster.internal/ubuntu noble/main riscv64 binutils riscv64 2.42-4ubuntu2 [2984 B]
Get:160 http://ftpmaster.internal/ubuntu noble/main riscv64 binutils-common riscv64 2.42-4ubuntu2 [209 kB]
Get:161 http://ftpmaster.internal/ubuntu noble/main riscv64 libsframe1 riscv64 2.42-4ubuntu2 [15.7 kB]
Get:162 http://ftpmaster.internal/ubuntu noble/main riscv64 libgomp1 riscv64 14-20240412-0ubuntu1 [145 kB]
Get:163 http://ftpmaster.internal/ubuntu noble/main riscv64 libatomic1 riscv64 14-20240412-0ubuntu1 [9488 B]
Get:164 http://ftpmaster.internal/ubuntu noble/main riscv64 libasan8 riscv64 14-20240412-0ubuntu1 [2626 kB]
Get:165 http://ftpmaster.internal/ubuntu noble/main riscv64 libubsan1 riscv64 14-20240412-0ubuntu1 [1079 kB]
Get:166 http://ftpmaster.internal/ubuntu noble/main riscv64 g++-13 riscv64 13.2.0-23ubuntu4 [14.5 kB]
Get:167 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc-13 riscv64 13.2.0-23ubuntu4 [453 kB]
Get:168 http://ftpmaster.internal/ubuntu noble/main riscv64 libstdc++-13-dev riscv64 13.2.0-23ubuntu4 [5668 kB]
Get:169 http://ftpmaster.internal/ubuntu noble/main riscv64 libgcc-13-dev riscv64 13.2.0-23ubuntu4 [3859 kB]
Get:170 http://ftpmaster.internal/ubuntu noble/main riscv64 libcc1-0 riscv64 14-20240412-0ubuntu1 [45.2 kB]
Get:171 http://ftpmaster.internal/ubuntu noble/main riscv64 cpp-13 riscv64 13.2.0-23ubuntu4 [1032 B]
Get:172 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc-13-base riscv64 13.2.0-23ubuntu4 [48.9 kB]
Get:173 http://ftpmaster.internal/ubuntu noble/main riscv64 libisl23 riscv64 0.26-3build1 [718 kB]
Get:174 http://ftpmaster.internal/ubuntu noble/main riscv64 libmpfr6 riscv64 4.2.1-1build1 [293 kB]
Get:175 http://ftpmaster.internal/ubuntu noble/main riscv64 libmpc3 riscv64 1.3.1-1build1 [59.7 kB]
Get:176 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc-13-riscv64-linux-gnu riscv64 13.2.0-23ubuntu4 [19.7 MB]
Get:177 http://ftpmaster.internal/ubuntu noble/main riscv64 g++-13-riscv64-linux-gnu riscv64 13.2.0-23ubuntu4 [11.6 MB]
Get:178 http://ftpmaster.internal/ubuntu noble/main riscv64 cpp-13-riscv64-linux-gnu riscv64 13.2.0-23ubuntu4 [10.3 MB]
Get:179 http://ftpmaster.internal/ubuntu noble/main riscv64 g++ riscv64 4:13.2.0-7ubuntu1 [1082 B]
Get:180 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc riscv64 4:13.2.0-7ubuntu1 [5016 B]
Get:181 http://ftpmaster.internal/ubuntu noble/main riscv64 cpp riscv64 4:13.2.0-7ubuntu1 [22.4 kB]
Get:182 http://ftpmaster.internal/ubuntu noble/main riscv64 cpp-riscv64-linux-gnu riscv64 4:13.2.0-7ubuntu1 [5316 B]
Get:183 http://ftpmaster.internal/ubuntu noble/main riscv64 gcc-riscv64-linux-gnu riscv64 4:13.2.0-7ubuntu1 [1202 B]
Get:184 http://ftpmaster.internal/ubuntu noble/main riscv64 g++-riscv64-linux-gnu riscv64 4:13.2.0-7ubuntu1 [960 B]
Get:185 http://ftpmaster.internal/ubuntu noble/main riscv64 dpkg-dev all 1.22.6ubuntu6 [1074 kB]
Get:186 http://ftpmaster.internal/ubuntu noble/main riscv64 libdpkg-perl all 1.22.6ubuntu6 [268 kB]
Get:187 http://ftpmaster.internal/ubuntu noble/main riscv64 patch riscv64 2.7.6-7build3 [113 kB]
Get:188 http://ftpmaster.internal/ubuntu noble/main riscv64 make riscv64 4.3-4.1build2 [178 kB]
Get:189 http://ftpmaster.internal/ubuntu noble/main riscv64 lto-disabled-list all 47 [12.4 kB]
Get:190 http://ftpmaster.internal/ubuntu noble/main riscv64 libfakeroot riscv64 1.33-1 [34.6 kB]
Get:191 http://ftpmaster.internal/ubuntu noble/main riscv64 fakeroot riscv64 1.33-1 [78.4 kB]
Get:192 http://ftpmaster.internal/ubuntu noble/main riscv64 liblockfile-bin riscv64 1.17-1build3 [11.6 kB]
Get:193 http://ftpmaster.internal/ubuntu noble/main riscv64 liblockfile1 riscv64 1.17-1build3 [7002 B]
Get:194 http://ftpmaster.internal/ubuntu noble/main riscv64 lockfile-progs riscv64 0.1.19build2 [8288 B]
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dpkg: libtirpc3:riscv64: dependency problems, but removing anyway as you requested:
 libnss-nisplus:riscv64 depends on libtirpc3 (>= 1.0.2).

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Adding 'diversion of /lib/riscv64-linux-gnu/libtirpc.so.3.0.0 to /lib/riscv64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64'
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dpkg: libdb5.3:riscv64: dependency problems, but removing anyway as you requested:
 libperl5.36:riscv64 depends on libdb5.3.
 libpam-modules:riscv64 depends on libdb5.3.
 apt-utils depends on libdb5.3.

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dpkg: libgdbm6:riscv64: dependency problems, but removing anyway as you requested:
 libperl5.36:riscv64 depends on libgdbm6 (>= 1.21).
 libgdbm-compat4:riscv64 depends on libgdbm6 (>= 1.16).

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dpkg: libgdbm-compat4:riscv64: dependency problems, but removing anyway as you requested:
 libperl5.36:riscv64 depends on libgdbm-compat4 (>= 1.18-3).

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dpkg: libssl3:riscv64: dependency problems, but removing anyway as you requested:
 systemd depends on libssl3 (>= 3.0.0).

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dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty
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dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty
dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty
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dpkg: warning: unable to delete old directory '/lib/riscv64-linux-gnu/security': Directory not empty
Setting up libpam-modules:riscv64 (1.5.3-5ubuntu5) ...
Installing new version of config file /etc/security/namespace.init ...
dpkg: libhogweed6:riscv64: dependency problems, but removing anyway as you requested:
 libgnutls30:riscv64 depends on libhogweed6 (>= 3.6).

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dpkg: libnettle8:riscv64: dependency problems, but removing anyway as you requested:
 libgnutls30:riscv64 depends on libnettle8 (>= 3.7~).

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dpkg: libgnutls30:riscv64: dependency problems, but removing anyway as you requested:
 apt depends on libgnutls30 (>= 3.7.5).

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dpkg: libapt-pkg6.0:riscv64: dependency problems, but removing anyway as you requested:
 apt-utils depends on libapt-pkg6.0 (>= 2.7.3).
 apt depends on libapt-pkg6.0 (>= 2.7.3).

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dpkg: warning: old file '/bin/bzcat' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2')
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dpkg: warning: old file '/bin/bunzip2' is the same as several new files! (both '/usr/bin/bzcat' and '/usr/bin/bzip2')
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dpkg: libreadline8:riscv64: dependency problems, but removing anyway as you requested:
 gpgconf depends on libreadline8 (>= 6.0).

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dpkg: libext2fs2:riscv64: dependency problems, but removing anyway as you requested:
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Current default time zone: 'Etc/UTC'
Local time is now:      Fri May 10 19:41:16 UTC 2024.
Universal Time is now:  Fri May 10 19:41:16 UTC 2024.
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Setting up gcc-13-riscv64-linux-gnu (13.2.0-23ubuntu4) ...
Setting up dpkg-dev (1.22.6ubuntu6) ...
Setting up gcc-riscv64-linux-gnu (4:13.2.0-7ubuntu1) ...
Setting up libtirpc-dev:riscv64 (1.3.4+ds-1.1build1) ...
Setting up gcc-13 (13.2.0-23ubuntu4) ...
Setting up cpp (4:13.2.0-7ubuntu1) ...
Setting up libnsl2:riscv64 (1.3.0-3build3) ...
Setting up g++-13-riscv64-linux-gnu (13.2.0-23ubuntu4) ...
Setting up g++-13 (13.2.0-23ubuntu4) ...
Setting up libnss-nisplus:riscv64 (1.3-5build1) ...
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Setting up g++-riscv64-linux-gnu (4:13.2.0-7ubuntu1) ...
Setting up libnss-nis:riscv64 (3.1-0ubuntu7) ...
Setting up g++ (4:13.2.0-7ubuntu1) ...
Setting up libnsl-dev:riscv64 (1.3.0-3build3) ...
Processing triggers for libc-bin (2.39-0ubuntu8) ...
Processing triggers for debianutils (5.17build1) ...
(Reading database ... 15729 files and directories currently installed.)
Purging configuration files for libssl3:riscv64 (3.0.10-1ubuntu2) ...
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Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-28173734 riscv64 noble -c chroot:build-PACKAGEBUILD-28173734 --arch=riscv64 --dist=noble --nolog fastml_3.11-4.dsc
Initiating build PACKAGEBUILD-28173734 with 4 jobs across 4 processor cores.
Kernel reported to sbuild: 6.5.0-28-generic #29.1~22.04.1-Ubuntu SMP Wed Apr 10 02:20:48 UTC 2024 riscv64
sbuild (Debian sbuild) 0.81.2ubuntu6 (16 February 2022) on bos03-riscv64-015.buildd

+==============================================================================+
| fastml 3.11-4 (riscv64)                      Fri, 10 May 2024 19:44:18 +0000 |
+==============================================================================+

Package: fastml
Version: 3.11-4
Source Version: 3.11-4
Distribution: noble
Machine Architecture: riscv64
Host Architecture: riscv64
Build Architecture: riscv64
Build Type: any

I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-28173734/chroot-autobuild' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/fastml-dymM9U/resolver-tSAq6d' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Local sources
-------------

fastml_3.11-4.dsc exists in .; copying to chroot
I: NOTICE: Log filtering will replace 'build/fastml-dymM9U/fastml-3.11' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/fastml-dymM9U' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [370 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [453 B]
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Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  apt-utils bash-completion ca-certificates debconf-i18n krb5-locales
  libgpg-error-l10n libgpm2 libgssapi-krb5-2 libip4tc2 libk5crypto3
  libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl libnsl-dev
  libnsl2 libnss-nis libnss-nisplus libperl5.36 libtext-charwidth-perl
  libtext-iconv-perl libtext-wrapi18n-perl libtirpc-common libtirpc-dev
  libtirpc3t64 libunistring2 openssl perl-modules-5.36 psmisc uuid-runtime
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf
  dh-strip-nondeterminism dwz file gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libdebhelper-perl libdw1t64 libelf1t64
  libfile-stripnondeterminism-perl libicu74 libmagic-mgc libmagic1t64
  libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
  po-debconf
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
  libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev debhelper debugedit dh-autoreconf
  dh-strip-nondeterminism dwz file gettext gettext-base groff-base
  intltool-debian libarchive-zip-perl libdebhelper-perl libdw1t64 libelf1t64
  libfile-stripnondeterminism-perl libicu74 libmagic-mgc libmagic1t64
  libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
  po-debconf sbuild-build-depends-main-dummy
0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.0 MB of archives.
After this operation, 67.0 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [664 B]
Get:2 http://ftpmaster.internal/ubuntu noble/main riscv64 libelf1t64 riscv64 0.190-1.1build4 [63.5 kB]
Get:3 http://ftpmaster.internal/ubuntu noble/main riscv64 libicu74 riscv64 74.2-1ubuntu3 [10.9 MB]
Get:4 http://ftpmaster.internal/ubuntu noble/main riscv64 libxml2 riscv64 2.9.14+dfsg-1.3ubuntu3 [719 kB]
Get:5 http://ftpmaster.internal/ubuntu noble/main riscv64 libmagic-mgc riscv64 1:5.45-3build1 [307 kB]
Get:6 http://ftpmaster.internal/ubuntu noble/main riscv64 libmagic1t64 riscv64 1:5.45-3build1 [96.4 kB]
Get:7 http://ftpmaster.internal/ubuntu noble/main riscv64 file riscv64 1:5.45-3build1 [21.9 kB]
Get:8 http://ftpmaster.internal/ubuntu noble/main riscv64 gettext-base riscv64 0.21-14ubuntu2 [42.6 kB]
Get:9 http://ftpmaster.internal/ubuntu noble/main riscv64 libuchardet0 riscv64 0.0.8-1build1 [77.8 kB]
Get:10 http://ftpmaster.internal/ubuntu noble/main riscv64 groff-base riscv64 1.23.0-3build2 [1031 kB]
Get:11 http://ftpmaster.internal/ubuntu noble/main riscv64 libpipeline1 riscv64 1.5.7-2 [30.9 kB]
Get:12 http://ftpmaster.internal/ubuntu noble/main riscv64 man-db riscv64 2.12.0-4build2 [1226 kB]
Get:13 http://ftpmaster.internal/ubuntu noble/main riscv64 m4 riscv64 1.4.19-4build1 [264 kB]
Get:14 http://ftpmaster.internal/ubuntu noble/main riscv64 autoconf all 2.71-3 [339 kB]
Get:15 http://ftpmaster.internal/ubuntu noble/main riscv64 autotools-dev all 20220109.1 [44.9 kB]
Get:16 http://ftpmaster.internal/ubuntu noble/main riscv64 automake all 1:1.16.5-1.3ubuntu1 [558 kB]
Get:17 http://ftpmaster.internal/ubuntu noble/main riscv64 autopoint all 0.21-14ubuntu2 [422 kB]
Get:18 http://ftpmaster.internal/ubuntu noble/main riscv64 libdebhelper-perl all 13.14.1ubuntu5 [89.8 kB]
Get:19 http://ftpmaster.internal/ubuntu noble/main riscv64 libtool all 2.4.7-7build1 [166 kB]
Get:20 http://ftpmaster.internal/ubuntu noble/main riscv64 dh-autoreconf all 20 [16.1 kB]
Get:21 http://ftpmaster.internal/ubuntu noble/main riscv64 libarchive-zip-perl all 1.68-1 [90.2 kB]
Get:22 http://ftpmaster.internal/ubuntu noble/main riscv64 libsub-override-perl all 0.10-1 [10.0 kB]
Get:23 http://ftpmaster.internal/ubuntu noble/main riscv64 libfile-stripnondeterminism-perl all 1.13.1-1 [18.1 kB]
Get:24 http://ftpmaster.internal/ubuntu noble/main riscv64 dh-strip-nondeterminism all 1.13.1-1 [5362 B]
Get:25 http://ftpmaster.internal/ubuntu noble/main riscv64 libdw1t64 riscv64 0.190-1.1build4 [275 kB]
Get:26 http://ftpmaster.internal/ubuntu noble/main riscv64 debugedit riscv64 1:5.0-5build2 [49.2 kB]
Get:27 http://ftpmaster.internal/ubuntu noble/main riscv64 dwz riscv64 0.15-1build6 [125 kB]
Get:28 http://ftpmaster.internal/ubuntu noble/main riscv64 gettext riscv64 0.21-14ubuntu2 [875 kB]
Get:29 http://ftpmaster.internal/ubuntu noble/main riscv64 intltool-debian all 0.35.0+20060710.6 [23.2 kB]
Get:30 http://ftpmaster.internal/ubuntu noble/main riscv64 po-debconf all 1.0.21+nmu1 [233 kB]
Get:31 http://ftpmaster.internal/ubuntu noble/main riscv64 debhelper all 13.14.1ubuntu5 [869 kB]
Preconfiguring packages ...
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Setting up libpipeline1:riscv64 (1.5.7-2) ...
Setting up libmagic-mgc (1:5.45-3build1) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.14.1ubuntu5) ...
Setting up libmagic1t64:riscv64 (1:5.45-3build1) ...
Setting up gettext-base (0.21-14ubuntu2) ...
Setting up m4 (1.4.19-4build1) ...
Setting up file (1:5.45-3build1) ...
Setting up libelf1t64:riscv64 (0.190-1.1build4) ...
Setting up libdw1t64:riscv64 (0.190-1.1build4) ...
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Setting up autopoint (0.21-14ubuntu2) ...
Setting up autoconf (2.71-3) ...
Setting up libicu74:riscv64 (74.2-1ubuntu3) ...
Setting up dwz (0.15-1build6) ...
Setting up libuchardet0:riscv64 (0.0.8-1build1) ...
Setting up debugedit (1:5.0-5build2) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libxml2:riscv64 (2.9.14+dfsg-1.3ubuntu3) ...
Setting up automake (1:1.16.5-1.3ubuntu1) ...
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 (0.21-14ubuntu2) ...
Setting up libtool (2.4.7-7build1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up groff-base (1.23.0-3build2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.12.0-4build2) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /usr/lib/systemd/system/man-db.timer.
Setting up debhelper (13.14.1ubuntu5) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.39-0ubuntu8) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (riscv64 included in any)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 6.5.0-28-generic #29.1~22.04.1-Ubuntu SMP Wed Apr 10 02:20:48 UTC 2024 riscv64 (riscv64)
Toolchain package versions: binutils_2.42-4ubuntu2 dpkg-dev_1.22.6ubuntu6 g++-13_13.2.0-23ubuntu4 gcc-13_13.2.0-23ubuntu4 libc6-dev_2.39-0ubuntu8 libstdc++-13-dev_13.2.0-23ubuntu4 libstdc++6_14-20240412-0ubuntu1 linux-libc-dev_6.8.0-31.31
Package versions: adduser_3.137ubuntu1 advancecomp_2.5-1build1 apt_2.7.14build2 apt-utils_2.7.14build2 autoconf_2.71-3 automake_1:1.16.5-1.3ubuntu1 autopoint_0.21-14ubuntu2 autotools-dev_20220109.1 base-files_13ubuntu10 base-passwd_3.6.3build1 bash_5.2.21-2ubuntu4 bash-completion_1:2.11-8 binutils_2.42-4ubuntu2 binutils-common_2.42-4ubuntu2 binutils-riscv64-linux-gnu_2.42-4ubuntu2 bsdextrautils_2.39.3-9ubuntu6 bsdutils_1:2.39.3-9ubuntu6 build-essential_12.10ubuntu1 bzip2_1.0.8-5.1 ca-certificates_20240203 coreutils_9.4-3ubuntu6 cpp_4:13.2.0-7ubuntu1 cpp-13_13.2.0-23ubuntu4 cpp-13-riscv64-linux-gnu_13.2.0-23ubuntu4 cpp-riscv64-linux-gnu_4:13.2.0-7ubuntu1 dash_0.5.12-6ubuntu5 debconf_1.5.86ubuntu1 debconf-i18n_1.5.86ubuntu1 debhelper_13.14.1ubuntu5 debianutils_5.17build1 debugedit_1:5.0-5build2 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1build1 dpkg_1.22.6ubuntu6 dpkg-dev_1.22.6ubuntu6 dwz_0.15-1build6 e2fsprogs_1.47.0-2.4~exp1ubuntu4 fakeroot_1.33-1 file_1:5.45-3build1 findutils_4.9.0-5build1 g++_4:13.2.0-7ubuntu1 g++-13_13.2.0-23ubuntu4 g++-13-riscv64-linux-gnu_13.2.0-23ubuntu4 g++-riscv64-linux-gnu_4:13.2.0-7ubuntu1 gcc_4:13.2.0-7ubuntu1 gcc-13_13.2.0-23ubuntu4 gcc-13-base_13.2.0-23ubuntu4 gcc-13-riscv64-linux-gnu_13.2.0-23ubuntu4 gcc-14-base_14-20240412-0ubuntu1 gcc-riscv64-linux-gnu_4:13.2.0-7ubuntu1 gettext_0.21-14ubuntu2 gettext-base_0.21-14ubuntu2 gpg_2.4.4-2ubuntu17 gpg-agent_2.4.4-2ubuntu17 gpgconf_2.4.4-2ubuntu17 gpgv_2.4.4-2ubuntu17 grep_3.11-4build1 groff-base_1.23.0-3build2 gzip_1.12-1ubuntu3 hostname_3.23+nmu2ubuntu2 init_1.66ubuntu1 init-system-helpers_1.66ubuntu1 intltool-debian_0.35.0+20060710.6 krb5-locales_1.20.1-6ubuntu2 libacl1_2.3.2-1build1 libapparmor1_4.0.0-beta3-0ubuntu3 libapt-pkg6.0t64_2.7.14build2 libarchive-zip-perl_1.68-1 libargon2-1_0~20190702+dfsg-4build1 libasan8_14-20240412-0ubuntu1 libassuan0_2.5.6-1build1 libatomic1_14-20240412-0ubuntu1 libattr1_1:2.5.2-1build1 libaudit-common_1:3.1.2-2.1build1 libaudit1_1:3.1.2-2.1build1 libbinutils_2.42-4ubuntu2 libblkid1_2.39.3-9ubuntu6 libbz2-1.0_1.0.8-5.1 libc-bin_2.39-0ubuntu8 libc-dev-bin_2.39-0ubuntu8 libc6_2.39-0ubuntu8 libc6-dev_2.39-0ubuntu8 libcap-ng0_0.8.4-2build2 libcap2_1:2.66-5ubuntu2 libcc1-0_14-20240412-0ubuntu1 libcom-err2_1.47.0-2.4~exp1ubuntu4 libcrypt-dev_1:4.4.36-4build1 libcrypt1_1:4.4.36-4build1 libcryptsetup12_2:2.7.0-1ubuntu4 libctf-nobfd0_2.42-4ubuntu2 libctf0_2.42-4ubuntu2 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.271ubuntu3 libdebhelper-perl_13.14.1ubuntu5 libdevmapper1.02.1_2:1.02.185-3ubuntu3 libdpkg-perl_1.22.6ubuntu6 libdw1t64_0.190-1.1build4 libelf1t64_0.190-1.1build4 libext2fs2t64_1.47.0-2.4~exp1ubuntu4 libfakeroot_1.33-1 libfdisk1_2.39.3-9ubuntu6 libffi8_3.4.6-1build1 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-13-dev_13.2.0-23ubuntu4 libgcc-s1_14-20240412-0ubuntu1 libgcrypt20_1.10.3-2build1 libgdbm-compat4t64_1.23-5.1build1 libgdbm6t64_1.23-5.1build1 libgmp10_2:6.3.0+dfsg-2ubuntu6 libgnutls30t64_3.8.3-1.1ubuntu3 libgomp1_14-20240412-0ubuntu1 libgpg-error-l10n_1.47-3build2 libgpg-error0_1.47-3build2 libgpm2_1.20.7-11 libgssapi-krb5-2_1.20.1-6ubuntu2 libhogweed6t64_3.9.1-2.2build1 libicu74_74.2-1ubuntu3 libidn2-0_2.3.7-2build1 libip4tc2_1.8.10-3ubuntu2 libisl23_0.26-3build1 libjansson4_2.14-2build2 libjson-c5_0.17-1build1 libk5crypto3_1.20.1-6ubuntu2 libkeyutils1_1.6.3-3build1 libkmod2_31+20240202-2ubuntu7 libkrb5-3_1.20.1-6ubuntu2 libkrb5support0_1.20.1-6ubuntu2 liblocale-gettext-perl_1.07-6ubuntu5 liblockfile-bin_1.17-1build3 liblockfile1_1.17-1build3 liblz4-1_1.9.4-1build1 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3build1 libmagic1t64_1:5.45-3build1 libmd0_1.1.0-2build1 libmount1_2.39.3-9ubuntu6 libmpc3_1.3.1-1build1 libmpfr6_4.2.1-1build1 libncursesw6_6.4+20240113-1ubuntu2 libnettle8t64_3.9.1-2.2build1 libnpth0t64_1.6-3.1build1 libnsl-dev_1.3.0-3build3 libnsl2_1.3.0-3build3 libnss-nis_3.1-0ubuntu7 libnss-nisplus_1.3-5build1 libp11-kit0_0.25.3-4ubuntu2 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sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2build1 sensible-utils_0.0.22 systemd_255.4-1ubuntu8 systemd-dev_255.4-1ubuntu8 systemd-sysv_255.4-1ubuntu8 sysvinit-utils_3.08-6ubuntu3 tar_1.35+dfsg-3build1 tzdata_2024a-2ubuntu1 ubuntu-keyring_2023.11.28.1 util-linux_2.39.3-9ubuntu6 uuid-runtime_2.39.3-9ubuntu6 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1ubuntu2

+------------------------------------------------------------------------------+
| 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 <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
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

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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 /<<PKGBUILDDIR>>
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
DEB_BUILD_OPTIONS=noautodbgsym parallel=4
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=build-PACKAGEBUILD-28173734
SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-28173734
SCHROOT_COMMAND=env
SCHROOT_GID=2501
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=build-PACKAGEBUILD-28173734
SCHROOT_UID=2001
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=unknown
USER=buildd
V=1

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -mLaunchpad Build Daemon <buildd@bos03-riscv64-015.buildd> -B -rfakeroot
dpkg-buildpackage: info: source package fastml
dpkg-buildpackage: info: source version 3.11-4
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture riscv64
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
	make -j4 clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
cd libs;make clean
cd programs;make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/libs'
cd phylogeny && make clean
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs'
cd fastml && make clean
cd gainLoss && make clean
cd indelCoder && make clean
make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/fastml'
rm -f libfastml.a libfastmlDebug.a libfastmlDoubleRep.a fastml  fastml.debug fastml.doubleRep *.o
make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/gainLoss'
rm -f libgainLoss.a libgainLossDebug.a libgainLossDoubleRep.a gainLoss  gainLoss.debug gainLoss.doubleRep *.o
make[4]: Entering directory '/<<PKGBUILDDIR>>/libs/phylogeny'
rm -f libEvolTree.a libEvolTreeDebug.a libEvolTreeDoubleRep.a   *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/fastml'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/gainLoss'
make[4]: Entering directory '/<<PKGBUILDDIR>>/programs/indelCoder'
rm -f libindelCoder.a libindelCoderDebug.a libindelCoderDoubleRep.a indelCoder  indelCoder.debug indelCoder.doubleRep *.o
make[4]: Leaving directory '/<<PKGBUILDDIR>>/libs/phylogeny'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/programs/indelCoder'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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 '/<<PKGBUILDDIR>>'
   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 -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd libs;make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/libs'
cd phylogeny && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/libs/phylogeny'
making depend
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o AddLog.o AddLog.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o NNiProp.o NNiProp.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o NNiSep.o NNiSep.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o Nni.o Nni.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o aaJC.o aaJC.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o allTrees.o allTrees.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o allTreesSeparateModel.o allTreesSeparateModel.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o alphabet.o alphabet.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o amino.o amino.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestAlpha.o bestAlpha.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestAlphaManyTrees.o bestAlphaManyTrees.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestHKYparam.o bestHKYparam.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;
      |                 ^~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bootstrap.o bootstrap.cpp
bestAlphaManyTrees.cpp: In function ‘void bestAlpha::optimizeAlphaNG_EM_PROP_n_alpha(tree&, std::vector<sequenceContainer>&, std::vector<stochasticProcess>&, const std::vector<std::vector<double>*>*, std::vector<double>&, 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
      |                       ^~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblEM.o bblEM.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblEMfixRoot.o bblEMfixRoot.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblEMProprtional.o bblEMProprtional.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblEMProportionalEB.o bblEMProportionalEB.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblLSProportionalEB.o bblLSProportionalEB.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblEMSeperate.o bblEMSeperate.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o chebyshevAccelerator.o chebyshevAccelerator.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o clustalFormat.o clustalFormat.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o codon.o codon.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o codonJC.o codonJC.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computeCounts.o computeCounts.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computeDownAlg.o computeDownAlg.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computeMarginalAlg.o computeMarginalAlg.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computePijComponent.o computePijComponent.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computeUpAlg.o computeUpAlg.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computeUpAlgFactors.o computeUpAlgFactors.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computeSubstitutionCounts.o computeSubstitutionCounts.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computePosteriorExpectationOfSubstitutions.o computePosteriorExpectationOfSubstitutions.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computePosteriorExpectationOfSubstitutions_nonReversibleSp.o computePosteriorExpectationOfSubstitutions_nonReversibleSp.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):
      | ^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o ConversionUtils.o ConversionUtils.cpp
In file included from /usr/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<char>]’,
    inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3:
/usr/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<char>]’,
    inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3:
/usr/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<char>]’,
    inlined from ‘double computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, double&, std::string)’ at computePosteriorExpectationOfSubstitutions_nonReversibleSp.cpp:76:3:
/usr/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<char>]’,
    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/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<char>]’,
    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/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<char>]’,
    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/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;
      |                                   ^~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o countTableComponent.o countTableComponent.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o datMatrixHolder.o datMatrixHolder.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o distanceTable.o distanceTable.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o distribution.o distribution.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o errorMsg.o errorMsg.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o evaluateCharacterFreq.o evaluateCharacterFreq.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fastStartTree.o fastStartTree.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fastaFormat.o fastaFormat.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o findRateOfGene.o findRateOfGene.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistance.o fromCountTableComponentToDistance.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistancefixRoot.o fromCountTableComponentToDistancefixRoot.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistanceProp.o fromCountTableComponentToDistanceProp.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistancePropEB.o fromCountTableComponentToDistancePropEB.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromQtoPt.o fromQtoPt.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o generalGammaDistributionFixedCategories.o generalGammaDistributionFixedCategories.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o gammaDistribution.o gammaDistribution.cpp
In file included from fromCountTableComponentToDistancePropEB.cpp:3:
fromCountTableComponentToDistancePropEB.h: In constructor ‘fromCountTableComponentToDistancePropEB::fromCountTableComponentToDistancePropEB(const std::vector<std::vector<countTableComponentGamProportional> >&, 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(
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o gammaUtilities.o gammaUtilities.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o generalGammaDistribution.o generalGammaDistribution.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o getRandomWeights.o getRandomWeights.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o goldmanYangModel.o goldmanYangModel.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o granthamChemicalDistances.o granthamChemicalDistances.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o hky.o hky.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):
      | ^~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o simulateWithDependence.o simulateWithDependence.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o KH_calculation.o KH_calculation.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likeDist.o likeDist.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likeDistfixRoot.o likeDistfixRoot.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 {
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likeDistProp.o likeDistProp.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;
      |             ^~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likeDistPropEB.o likeDistPropEB.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likelihoodComputation.o likelihoodComputation.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likelihoodComputationFactors.o likelihoodComputationFactors.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o logFile.o logFile.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o maseFormat.o maseFormat.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o molphyFormat.o molphyFormat.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o nexusFormat.o nexusFormat.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;
      |                 ^~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o nj.o nj.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o njConstrain.o njConstrain.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o nucJC.o nucJC.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o nucleotide.o nucleotide.cpp
In file included from /usr/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
      |           ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -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<n;i++) e[i-1]=e[i];
      |   
numRec.cpp:307:2: warning: "/*" within comment [-Wcomment]
  307 | //*     e[n-1]=0.0;
      |   
numRec.cpp:308:2: warning: "/*" within comment [-Wcomment]
  308 | //*     e.push_back(0);//since in my algorithm I return an n-1 sized e
      |   
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o Parameters.o Parameters.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o phylipFormat.o phylipFormat.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o pijAccelerator.o pijAccelerator.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o readDatMatrix.o readDatMatrix.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o readTree.o readTree.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o recognizeFormat.o recognizeFormat.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o replacementModel.o replacementModel.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o searchStatus.o searchStatus.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o seqContainerTreeMap.o seqContainerTreeMap.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o sequence.o sequence.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o sequenceContainer.o sequenceContainer.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))
      |                    ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<std::__cxx11::basic_string<char> > sequenceContainer::getSeqNamesThatMatchPos(int, char)’:
sequenceContainer.cpp:467:19: warning: unused variable ‘len’ [-Wunused-variable]
  467 |         const int len = _seqDataVec[0].seqLen();
      |                   ^~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o simulateTree.o simulateTree.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o siteSpecificRate.o siteSpecificRate.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o someUtil.o someUtil.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o split.o split.cpp
someUtil.cpp: In function ‘void createDir(const std::string&, const std::string&)’:
someUtil.cpp:520:23: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
  520 |                 system(sysCall.c_str());
      |                 ~~~~~~^~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o splitMap.o splitMap.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o splitTreeUtil.o splitTreeUtil.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o stochasticProcess.o stochasticProcess.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o suffStatComponent.o suffStatComponent.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o talRandom.o talRandom.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o tree.o tree.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o treeIt.o treeIt.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o treeUtil.o treeUtil.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o uniDistribution.o uniDistribution.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();
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o uniformDistribution.o uniformDistribution.cpp
treeUtil.cpp: In function ‘std::vector<tree> 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();
      |                                ^~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o cmdline2EvolObjs.o cmdline2EvolObjs.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o generalGammaDistributionLaguerre.o generalGammaDistributionLaguerre.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o gammaDistributionLaguerre.o gammaDistributionLaguerre.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o GLaguer.o GLaguer.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o givenRatesMLDistance.o givenRatesMLDistance.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o distanceBasedSeqs2Tree.o distanceBasedSeqs2Tree.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o posteriorDistance.o posteriorDistance.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o pairwiseGammaDistance.o pairwiseGammaDistance.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o doubleRep.o doubleRep.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o logRep.o logRep.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o indel.o indel.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,
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
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>*, 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*, double*) const’
   32 |     const MDOUBLE giveDistance(const sequence& s1,
      |                   ^~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o indelModel.o indelModel.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o mulAlphabet.o mulAlphabet.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o replacementModelSSRV.o replacementModelSSRV.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o stochasticProcessSSRV.o stochasticProcessSSRV.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestAlphaAndNu.o bestAlphaAndNu.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o C_evalParamUSSRV.o C_evalParamUSSRV.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o matrixUtils.o matrixUtils.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o betaOmegaDistribution.o betaOmegaDistribution.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o betaUtilities.o betaUtilities.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o betaDistribution.o betaDistribution.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o geneticCodeHolder.o geneticCodeHolder.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<MDOUBLE> _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) :
      | ^~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o samplingSequences.o samplingSequences.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblEM2USSRV.o bblEM2USSRV.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestParamUSSRV.o bestParamUSSRV.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likeDist2USSRV.o likeDist2USSRV.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o ussrvModel.o ussrvModel.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likelihoodComputation2USSRV.o likelihoodComputation2USSRV.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistance2USSRV.o fromCountTableComponentToDistance2USSRV.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o normalDist.o normalDist.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o tamura92.o tamura92.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestTamura92param.o bestTamura92param.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o phylipSequentialFormat.o phylipSequentialFormat.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o simulateCodonsJumps.o simulateCodonsJumps.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o simulateJumpsAbstract.o simulateJumpsAbstract.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o ssrvDistanceSeqs2Tree.o ssrvDistanceSeqs2Tree.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o multipleStochasticProcess.o multipleStochasticProcess.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o distributionPlusInvariant.o distributionPlusInvariant.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o extremeValDistribution.o extremeValDistribution.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o gammaDistributionFixedCategories.o gammaDistributionFixedCategories.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o generalGammaDistributionPlusInvariant.o generalGammaDistributionPlusInvariant.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o gammaDistributionPlusInvariant.o gammaDistributionPlusInvariant.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o distributionPlusCategory.o distributionPlusCategory.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 {
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o simulateJumps.o simulateJumps.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o computeJumps.o computeJumps.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 {
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o seqeuncesFilter.o seqeuncesFilter.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o optGammaMixtureLS.o optGammaMixtureLS.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)
      | ^~~~~~~~~~~~
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();
      |                         ^~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o mixtureDistribution.o mixtureDistribution.cpp
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;
      |             ^~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o suffStatGammaMixture.o suffStatGammaMixture.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o GamMixtureOptimizer.o GamMixtureOptimizer.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;
      |                           ^~~~~~~~~~~~~~~~~~~
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;
      |                 ^~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o optGammaMixtureEM.o optGammaMixtureEM.cpp
In file included from /usr/include/riscv64-linux-gnu/c++/13/bits/c++allocator.h:33,
                 from /usr/include/c++/13/bits/allocator.h:46,
                 from /usr/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<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]’ at /usr/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<generalGammaDistribution*>]’ at /usr/include/c++/13/bits/stl_vector.h:1286:30,
    inlined from ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’ at mixtureDistribution.cpp:84:24:
/usr/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/include/c++/13/vector:66:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = generalGammaDistribution*; _Alloc = std::allocator<generalGammaDistribution*>]’,
    inlined from ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’ at mixtureDistribution.cpp:84:24:
/usr/include/c++/13/bits/stl_vector.h:1292:28: warning: ‘pComp’ may be used uninitialized [-Wmaybe-uninitialized]
 1292 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/13/vector:72:
/usr/include/c++/13/bits/vector.tcc: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, Vdouble, Vdouble, Vdouble, quadratureType, double, double)’:
/usr/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<generalGammaDistribution*>]’ 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<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = generalGammaDistribution*; _Args = {generalGammaDistribution* const&}; _Tp = generalGammaDistribution*]’ at /usr/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<generalGammaDistribution*>]’ at /usr/include/c++/13/bits/stl_vector.h:1286:30,
    inlined from ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’ at mixtureDistribution.cpp:52:24:
/usr/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<generalGammaDistribution*>]’,
    inlined from ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’ at mixtureDistribution.cpp:52:24:
/usr/include/c++/13/bits/stl_vector.h:1292:28: warning: ‘pComp’ may be used uninitialized [-Wmaybe-uninitialized]
 1292 |           _M_realloc_insert(end(), __x);
      |           ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In constructor ‘mixtureDistribution::mixtureDistribution(int, int, quadratureType, double, double)’:
/usr/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<generalGammaDistribution*>]’ declared here
  445 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
mixtureDistribution.cpp:40:43: note: ‘pComp’ declared here
   40 |                 generalGammaDistribution* pComp;
      |                                           ^~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o gainLossAlphabet.o gainLossAlphabet.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)));
      |                         ^~~~~~~~
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)));
      |                         ^~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o wYangModel.o wYangModel.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o codonUtils.o codonUtils.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likelihoodComputation2Codon.o likelihoodComputation2Codon.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likeDist2Codon.o likeDist2Codon.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o unObservableData.o unObservableData.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o likelihoodComputationGL.o likelihoodComputationGL.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o threeStateModel.o threeStateModel.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o threeStateAlphabet.o threeStateAlphabet.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o oneTwoMoreModel.o oneTwoMoreModel.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o betaDistributionFixedCategories.o betaDistributionFixedCategories.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o betaDistributionFixedCategoriesWithOmegaUniform.o betaDistributionFixedCategoriesWithOmegaUniform.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bblEM2codon.o bblEM2codon.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestAlphaAndK.o bestAlphaAndK.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o fromCountTableComponentToDistance2Codon.o fromCountTableComponentToDistance2Codon.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -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,
      | ^~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o bestGtrModelParams.o bestGtrModelParams.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o simulateRateShiftJumps.o simulateRateShiftJumps.cpp
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;
      |                 ^~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -DLOG   -c -o integerAlphabet.o integerAlphabet.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,
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~
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 '/<<PKGBUILDDIR>>/libs/phylogeny'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/libs'
cd programs;make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/programs'
cd fastml && make all
cd gainLoss && make all
cd indelCoder && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/fastml'
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/gainLoss'
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/indelCoder'
making depend
making depend
making depend
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o indelCoder.o indelCoder.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o indelCoderOptions.o indelCoderOptions.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o fastml.o fastml.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();
      |             ^~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbAlg.o bbAlg.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)
      |                  ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLossOptions.o gainLossOptions.cpp
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() {
      |                     ^~~~~~~~~~~~~~~~~~~
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)
      |                  ^~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLoss.o gainLoss.cpp
bbAlg.h: In constructor ‘bbAlg::bbAlg(const tree&, std::vector<stochasticProcess>&, 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() {
      |                     ^~~~~~~~~~~~~~~~~~~
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;
      |                      ^~~~~~~~~
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<std::vector<stochasticProcess*> >&, 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<vector<stochasticProcess*> >& spVVec,
      |                  ^~~~~~~~~~~~~~
bblLS.h: In constructor ‘evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, 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<vector<stochasticProcess*> >& 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()){
      |                                             ^~~~~~~~~~~~~~~~~~~
      |                                             (                  )
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;
      |                        ^~~~~~~~~~
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<std::vector<stochasticProcess*> >&, distribution*, distribution*, unObservableData*, std::ostream&)’:
gainLoss.cpp:1990:25: warning: unused variable ‘sumPijQij’ [-Wunused-variable]
 1990 |                 MDOUBLE sumPijQij = normalizeQ(spVVec,gainDist,lossDist);
      |                         ^~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbComputeDownAlg.o bbComputeDownAlg.cpp
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;
      |                                 ^~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o indelCoderProject.o indelCoderProject.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::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;
      |                        ^~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbComputeUpAlg.o bbComputeUpAlg.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o indelCoderUtils.o indelCoderUtils.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLossUtils.o gainLossUtils.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbEvaluateSpecificAV.o bbEvaluateSpecificAV.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<std::vector<stochasticProcess*> >&, 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<std::vector<stochasticProcess*> >&, distribution*, distribution*)’:
gainLossUtils.cpp:788:17: warning: unused variable ‘scale’ [-Wunused-variable]
  788 |         MDOUBLE scale;
      |                 ^~~~~
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,
      | ^~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o character.o character.cpp
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() {
      |                     ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbfindBestAVDynProg.o bbfindBestAVDynProg.cpp
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;
      |                 ^~~
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;
      |                 ^~~~~~
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;
      |             ^~~~~~~~~~~~~~~~~
gainLoss.cpp: In member function ‘void gainLoss::initParamsAtRandPointsSPvv(int, std::vector<std::vector<stochasticProcess*> >&, 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;
      |                 ^~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gaps.o gaps.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() {
      |                     ^~~~~~~~~~~~~~~~~~~
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
g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libindelCoder.a ../../libs/phylogeny/libEvolTree.a -o indelCoder
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbNodeOrderAlg.o bbNodeOrderAlg.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/indelCoder'
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bb_options.o bb_options.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o optimizeGainLossModel.o optimizeGainLossModel.cpp
In file included from /usr/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<char>]’,
    inlined from ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’ at gainLoss.cpp:3896:33:
/usr/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<char>]’,
    inlined from ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’ at gainLoss.cpp:3896:62:
/usr/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<char>]’,
    inlined from ‘void gainLoss::printLikelihoodLandscape(stochasticProcess*)’ at gainLoss.cpp:3896:74:
/usr/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;
      |                                     ^~~~~
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[]):
      | ^~~~~~~~~~
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,
      | ^~~~~~~~~~~~~~
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() {
      |                     ^~~~~~~~~~~~~~~~~~~
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;
      |                           ^~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bbReport.o bbReport.cpp
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() {
      |                     ^~~~~~~~~~~~~~~~~~~
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;
      |                          ^~~~~~~~
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;
      |                 ^~~~~~~~~
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 ) :
      | ^~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o computeMarginalReconstruction.o computeMarginalReconstruction.cpp
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;
      |                                       ^~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o optimizeGainLossModelVV.o optimizeGainLossModelVV.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;
      |                         ^~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o jointNoGamma.o jointNoGamma.cpp
computeMarginalReconstruction.cpp:45:17: warning: unused variable ‘totalLikelihoodOfReconstruction’ [-Wunused-variable]
   45 |         MDOUBLE totalLikelihoodOfReconstruction = 0;
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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<std::vector<stochasticProcess*> >&, 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;
      |                 ^~~~~~~~~
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<int> jointNoGamma::computeJointAncestralFromSSC(int, const suffStatGlobalHomPos&, const suffStatGlobalHomPosJointNoGamma&, doubleRep&)’:
jointNoGamma.cpp:108:33: warning: unused variable ‘maxL’ [-Wunused-variable]
  108 |                         MDOUBLE maxL = VERYSMALL;
      |                                 ^~~~
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;
      |                                 ^~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o mainbb.o mainbb.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o sequenceDataDiff.o sequenceDataDiff.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLossModel.o gainLossModel.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 ../../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):
      | ^~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o suffStatComponentJointNoGamma.o suffStatComponentJointNoGamma.cpp
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() {
      |                     ^~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o siteSpecificGL.o siteSpecificGL.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -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 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)
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
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)
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLossProject.o gainLossProject.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLossOptimizer.o gainLossOptimizer.cpp
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;
      |                            ^~
In file included from /usr/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<char>]’,
    inlined from ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’ at computePosteriorExpectationOfChange.cpp:230:3:
/usr/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<char>]’,
    inlined from ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’ at computePosteriorExpectationOfChange.cpp:230:3:
/usr/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<char>]’,
    inlined from ‘double computePosteriorExpectationOfChange::computePosterioGivenTerminalsPerBranch(int, int, int, suffStatGlobalHomPos&, suffStatGlobalGamPos&, computePijHom&, doubleRep&, std::string)’ at computePosteriorExpectationOfChange.cpp:230:3:
/usr/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;
      |                 ^~~
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
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)
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libfastml.a ../../libs/phylogeny/libEvolTree.a -o fastml
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)
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
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<std::vector<stochasticProcess*> >&, 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<vector<stochasticProcess*> >& spVVec,
      |                  ^~~~~~~~~~~~~~
bblLS.h: In constructor ‘evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, 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<vector<stochasticProcess*> >& 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<std::vector<stochasticProcess*> >&, 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<vector<stochasticProcess*> >& 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<vector<stochasticProcess*> >& 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<vector<stochasticProcess*> >& 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;
      |                 ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o ancestralReconstructStates.o ancestralReconstructStates.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o rate4siteGL.o rate4siteGL.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/fastml'
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o computeCountsGL.o computeCountsGL.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)
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
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)
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
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;
      |             ^~~~~~~~~~~~
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;
      |                                           ^~~
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<std::vector<stochasticProcess*> >&, 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<vector<stochasticProcess*> >& 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<vector<stochasticProcess*> >& spVVec, distribution* gainDist, distribution* lossDist, string& outDir, VVVdouble& logLpostPerSpPerCatPerPos, MDOUBLE distanceFromNearestOTUForRecent, bool isSilent):
      | ^~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o computeCorrelations.o computeCorrelations.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o gainLoss4site.o gainLoss4site.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o simulateChangesAlongTree.o simulateChangesAlongTree.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)
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
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 {
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
      |             ^~~~~~~~~~~~~
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 ‘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<std::vector<bool> >&, VVVVdouble&, VVVdouble&, std::map<int, std::map<int, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, 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){
      |            ^~~~~~~~~~~~~
      |            (            )
gainLoss4site.h: In constructor ‘gainLoss4site::gainLoss4site(sequenceContainer&, tree&, std::vector<std::vector<stochasticProcess*> >, 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<std::vector<stochasticProcess*> > gainLoss4site::_spVVec’ [-Wreorder]
   61 |         vector<vector<stochasticProcess*> > _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,
      | ^~~~~~~~~~~~~
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<int, std::map<int, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> > > >&, std::vector<std::vector<bool> >&, 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();
      |              ^~~~~~~~
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)
      |                  ^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o simulateOnePos.o simulateOnePos.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o bblLS.o bblLS.cpp
g++ -g -O2 -fno-omit-frame-pointer -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fno-stack-clash-protection -fdebug-prefix-map=/<<PKGBUILDDIR>>=/usr/src/fastml-3.11-4 -O3 -Wall -Wno-sign-compare -I. -I../../libs/phylogeny -DLOG   -c -o sankoffReconstructGL.o sankoffReconstructGL.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 ../../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<std::vector<stochasticProcess*> >&, 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<vector<stochasticProcess*> >& spVVec,
      |                  ^~~~~~~~~~~~~~
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 {
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bblLS.h: In constructor ‘evalBranchProportionExponentSPvv::evalBranchProportionExponentSPvv(tree*, const sequenceContainer&, std::vector<std::vector<stochasticProcess*> >&, 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<vector<stochasticProcess*> >& 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<std::vector<stochasticProcess*> >&, 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)
      |                     ^~~~
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;
      |                                 ^~~~~~
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):
      | ^~~~~~~~~~~~~~~~~~~~
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<freqOfHighCorrPrev && Nmin_lower < medianNminOfRealData){
      |                                 ^~
computeCorrelations.cpp:406:25: note: ‘expextedFreq’ was declared here
  406 |                 MDOUBLE expextedFreq;
      |                         ^~~~~~~~~~~~
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
g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -L../../libs/phylogeny libgainLoss.a ../../libs/phylogeny/libEvolTree.a -o gainLoss
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/gainLoss'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/programs'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/fastml AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd libs;make all
make[2]: Entering directory '/<<PKGBUILDDIR>>/libs'
cd phylogeny && make all
make[3]: Entering directory '/<<PKGBUILDDIR>>/libs/phylogeny'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/libs/phylogeny'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/libs'
cd programs;make install
make[2]: Entering directory '/<<PKGBUILDDIR>>/programs'
cd fastml && make install
cd gainLoss && make install
cd indelCoder && make install
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/fastml'
mkdir -p ../../bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/gainLoss'
mkdir -p ../../bin
cp fastml ../../bin/fastml
make[3]: Entering directory '/<<PKGBUILDDIR>>/programs/indelCoder'
mkdir -p ../../bin
cp gainLoss ../../bin/gainLoss
cp indelCoder ../../bin/indelCoder
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/indelCoder'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/fastml'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/programs/gainLoss'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/programs'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   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
debugedit: debian/fastml/usr/bin/fastml: Unknown DWARF DW_FORM_0x1f20
a74d2457eabf7e5206a1717d1365b625ccbce77b
debugedit: debian/fastml/usr/bin/gainLoss: Unknown DWARF DW_FORM_0x1f21
98c13099d3898bcebfacbdd4059c58a77361c16b
debugedit: debian/fastml/usr/bin/indelCoder: Unknown DWARF DW_FORM_0x1f21
d973f10a590257ece423f741da75edad70220af9
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 from: /lib/ld-linux-riscv64-lp64d.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
 diversion by libc6 to: /lib/ld-linux-riscv64-lp64d.so.1.usr-is-merged
   dh_installdeb -a
   dh_gencontrol -a
   dh_md5sums -a
   dh_builddeb -a
INFO: pkgstriptranslations version 154
pkgstriptranslations: processing fastml (in debian/fastml); do_strip: , oemstrip: 
pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>"
pkgstripfiles: processing control file: debian/fastml/DEBIAN/control, package fastml, directory debian/fastml
pkgstripfiles: Running PNG optimization (using 4 cpus) for package fastml ...
pkgstripfiles: No PNG files.
dpkg-deb: building package 'fastml' in '../fastml_3.11-4_riscv64.deb'.
 dpkg-genbuildinfo --build=any -O../fastml_3.11-4_riscv64.buildinfo
 dpkg-genchanges --build=any -mLaunchpad Build Daemon <buildd@bos03-riscv64-015.buildd> -O../fastml_3.11-4_riscv64.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 2024-05-10T20:19:38Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


fastml_3.11-4_riscv64.changes:
------------------------------

Format: 1.8
Date: Wed, 24 Jan 2024 17:23:21 +0100
Source: fastml
Binary: fastml
Built-For-Profiles: noudeb
Architecture: riscv64
Version: 3.11-4
Distribution: noble
Urgency: medium
Maintainer: Launchpad Build Daemon <buildd@bos03-riscv64-015.buildd>
Changed-By: Andreas Tille <tille@debian.org>
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
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Files:
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/<<BUILDDIR>>/fastml_3.11-4_riscv64.changes.new could not be renamed to /<<BUILDDIR>>/fastml_3.11-4_riscv64.changes: Illegal seek
Distribution field may be wrong!!!
+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: fastml
Binary: fastml
Architecture: riscv64
Version: 3.11-4
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Build-Origin: Ubuntu
Build-Architecture: riscv64
Build-Date: Fri, 10 May 2024 20:19:33 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
 merged-usr-via-aliased-dirs
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 SOURCE_DATE_EPOCH="1706113401"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


fastml_3.11-4_riscv64.deb
-------------------------

 new Debian package, version 2.0.
 size 1026292 bytes: control archive=1165 bytes.
    1515 bytes,    27 lines      control
     494 bytes,     8 lines      md5sums
 Package: fastml
 Version: 3.11-4
 Architecture: riscv64
 Maintainer: Ubuntu Developers <ubuntu-devel-discuss@lists.ubuntu.com>
 Original-Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 2710
 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.4), libstdc++6 (>= 13.1)
 Section: science
 Priority: optional
 Homepage: http://fastml.tau.ac.il/
 Description: maximum likelihood ancestral amino-acid sequence reconstruction
  FastML is a bioinformatics tool for the reconstruction of ancestral
  sequences based on the phylogenetic relations between homologous
  sequences. FastML runs several algorithms that reconstruct the ancestral
  sequences with emphasis on an accurate reconstruction of both indels and
  characters. For character reconstruction the previously described FastML
  algorithms are used to efficiently infer the most likely ancestral
  sequences for each internal node of the tree. Both joint and the
  marginal reconstructions are provided. For indels reconstruction the
  sequences are first coded according to the indel events detected within
  the multiple sequence alignment (MSA) and then a state-of-the-art
  likelihood model is used to reconstruct ancestral indels states. The
  results are the most probable sequences, together with posterior
  probabilities for each character and indel at each sequence position for
  each internal node of the tree. FastML is generic and is applicable for
  any type of molecular sequences (nucleotide, protein, or codon
  sequences).

drwxr-xr-x root/root         0 2024-01-24 16:23 ./
drwxr-xr-x root/root         0 2024-01-24 16:23 ./usr/
drwxr-xr-x root/root         0 2024-01-24 16:23 ./usr/bin/
-rwxr-xr-x root/root    952672 2024-01-24 16:23 ./usr/bin/fastml
-rwxr-xr-x root/root   1562976 2024-01-24 16:23 ./usr/bin/gainLoss
-rwxr-xr-x root/root    239968 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


+------------------------------------------------------------------------------+
| Post Build                                                                   |
+------------------------------------------------------------------------------+


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not removing build depends: as requested

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: riscv64
Build Type: any
Build-Space: 671788
Build-Time: 1986
Distribution: noble
Host Architecture: riscv64
Install-Time: 102
Job: fastml_3.11-4.dsc
Machine Architecture: riscv64
Package: fastml
Package-Time: 2120
Source-Version: 3.11-4
Space: 671788
Status: successful
Version: 3.11-4
--------------------------------------------------------------------------------
Finished at 2024-05-10T20:19:38Z
Build needed 00:35:20, 671788k disk space
RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=noble --arch=riscv64 PACKAGEBUILD-28173734
Scanning for processes to kill in build PACKAGEBUILD-28173734