https://launchpad.net/ubuntu/+source/augustus/3.4.0+dfsg2-3build1/+build/22599315 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-059 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:52 UTC 2021 aarch64 Buildd toolchain package versions: launchpad-buildd_204~508~ubuntu18.04.1 python3-lpbuildd_204~508~ubuntu18.04.1 sbuild_0.75.0-1ubuntu1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu16.04.1 bzr_2.7.0+bzr6622-10 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu18.04.1 git_1:2.17.1-1ubuntu0.9 dpkg-dev_1.19.0.5ubuntu2.3 python-debian_0.1.32 python3-debian_0.1.32. Syncing the system clock with the buildd NTP service... 7 Dec 17:36:27 ntpdate[1684]: adjust time server 10.211.37.1 offset 0.009095 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599315 --image-type chroot /home/buildd/filecache-default/c698bf6badd89264039f6cdfcd7c983f87611a3e Creating target for build PACKAGEBUILD-22599315 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599315 Starting target for build PACKAGEBUILD-22599315 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599315 'deb http://ftpmaster.internal/ubuntu jammy main universe' 'deb http://ftpmaster.internal/ubuntu jammy-security main universe' 'deb http://ftpmaster.internal/ubuntu jammy-updates main universe' 'deb http://ftpmaster.internal/ubuntu jammy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-22599315 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599315 Updating target for build PACKAGEBUILD-22599315 Get:1 http://ftpmaster.internal/ubuntu jammy InRelease [270 kB] Get:2 http://ftpmaster.internal/ubuntu jammy-security InRelease [90.7 kB] Get:3 http://ftpmaster.internal/ubuntu jammy-updates InRelease [90.7 kB] Get:4 http://ftpmaster.internal/ubuntu jammy-proposed InRelease [121 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf Packages [1351 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main Translation-en [511 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/universe armhf Packages [12.8 MB] Get:8 http://ftpmaster.internal/ubuntu jammy/universe Translation-en [5567 kB] Get:9 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf Packages [141 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main Translation-en [51.2 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf Packages [585 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/universe Translation-en [312 kB] Fetched 21.9 MB in 7s (2956 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be REMOVED: libsemanage1* The following NEW packages will be installed: libsemanage2 libsepol2 libssl3 The following packages will be upgraded: apt base-files bash binutils binutils-arm-linux-gnueabihf binutils-common bsdutils bzip2 ca-certificates cpp-11 dash debconf debianutils dpkg dpkg-dev e2fsprogs g++-11 gcc-11 gcc-11-base gpg gpg-agent gpgconf gpgv grep libapparmor1 libapt-pkg6.0 libasan6 libatomic1 libattr1 libbinutils libblkid1 libbz2-1.0 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdpkg-perl libext2fs2 libgcc-11-dev libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libip4tc2 libisl23 libk5crypto3 libkmod2 libkrb5-3 libkrb5support0 libmount1 libmpc3 libncurses6 libncursesw6 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++-11-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libubsan1 libudev1 libuuid1 libzstd1 linux-libc-dev lockfile-progs login logsave lto-disabled-list make mount ncurses-base ncurses-bin openssl passwd pkgbinarymangler sensible-utils systemd systemd-sysv systemd-timesyncd tzdata usrmerge util-linux 101 upgraded, 3 newly installed, 1 to remove and 0 not upgraded. Need to get 69.3 MB of archives. After this operation, 337 MB disk space will be freed. Get:1 http://ftpmaster.internal/ubuntu jammy/main armhf debconf all 1.5.79 [126 kB] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf libpam0g armhf 1.4.0-10ubuntu2 [56.0 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt-dev armhf 1:4.4.26-1 [122 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main armhf libcrypt1 armhf 1:4.4.26-1 [94.1 kB] Get:5 http://ftpmaster.internal/ubuntu jammy/main armhf base-files armhf 12ubuntu2 [63.0 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf debianutils armhf 5.5-1ubuntu1 [106 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf bash armhf 5.1-5ubuntu1 [655 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf bsdutils armhf 1:2.37.2-4ubuntu1 [86.9 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf libgpg-error0 armhf 1.42-3 [60.1 kB] Get:10 http://ftpmaster.internal/ubuntu jammy/main armhf libgcrypt20 armhf 1.9.4-3ubuntu2 [438 kB] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf bzip2 armhf 1.0.8-5 [34.2 kB] Get:12 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libbz2-1.0 armhf 1.0.8-5 [31.7 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf libcc1-0 armhf 11.2.0-12ubuntu1 [45.8 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11-base armhf 11.2.0-12ubuntu1 [20.7 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf libgcc-s1 armhf 11.2.0-12ubuntu1 [42.6 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main armhf libgomp1 armhf 11.2.0-12ubuntu1 [101 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main armhf libatomic1 armhf 11.2.0-12ubuntu1 [7624 B] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf libasan6 armhf 11.2.0-12ubuntu1 [2242 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf libubsan1 armhf 11.2.0-12ubuntu1 [894 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf g++-11 armhf 11.2.0-12ubuntu1 [9005 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main armhf libstdc++-11-dev armhf 11.2.0-12ubuntu1 [2180 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main armhf libgcc-11-dev armhf 11.2.0-12ubuntu1 [839 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main armhf gcc-11 armhf 11.2.0-12ubuntu1 [15.8 MB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf cpp-11 armhf 11.2.0-12ubuntu1 [7833 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf libstdc++6 armhf 11.2.0-12ubuntu1 [573 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf libisl23 armhf 0.24-2 [581 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf libmpc3 armhf 1.2.1-1 [39.5 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf libzstd1 armhf 1.4.8+dfsg-3 [285 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf libctf0 armhf 2.37-10ubuntu1 [93.7 kB] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf libctf-nobfd0 armhf 2.37-10ubuntu1 [93.8 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf libbinutils armhf 2.37-10ubuntu1 [492 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main armhf binutils-common armhf 2.37-10ubuntu1 [213 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main armhf binutils armhf 2.37-10ubuntu1 [3174 B] Get:34 http://ftpmaster.internal/ubuntu jammy/main armhf binutils-arm-linux-gnueabihf armhf 2.37-10ubuntu1 [3057 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main armhf libssl3 armhf 3.0.0-1ubuntu1 [1575 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/main armhf libblkid1 armhf 2.37.2-4ubuntu1 [136 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/main armhf libuuid1 armhf 2.37.2-4ubuntu1 [23.3 kB] Get:38 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libcryptsetup12 armhf 2:2.4.2-1ubuntu3 [186 kB] Get:39 http://ftpmaster.internal/ubuntu jammy/main armhf libidn2-0 armhf 2.3.2-2 [67.8 kB] Get:40 http://ftpmaster.internal/ubuntu jammy/main armhf libp11-kit0 armhf 0.24.0-6 [219 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/main armhf libtasn1-6 armhf 4.18.0-4 [36.3 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main armhf libgnutls30 armhf 3.7.2-2ubuntu1 [923 kB] Get:43 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd-timesyncd armhf 249.5-2ubuntu1 [30.8 kB] Get:44 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd-sysv armhf 249.5-2ubuntu1 [10.5 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main armhf libapparmor1 armhf 3.0.3-0ubuntu4 [32.3 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main armhf libip4tc2 armhf 1.8.7-1ubuntu4 [17.7 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main armhf libkmod2 armhf 28-1ubuntu5 [40.9 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main armhf libpcre2-8-0 armhf 10.39-3 [190 kB] Get:49 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libselinux1 armhf 3.3-1build1 [66.7 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main armhf libmount1 armhf 2.37.2-4ubuntu1 [151 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main armhf libseccomp2 armhf 2.5.2-2ubuntu2 [47.7 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main armhf login armhf 1:4.8.1-2ubuntu1 [186 kB] Get:53 http://ftpmaster.internal/ubuntu jammy/main armhf util-linux armhf 2.37.2-4ubuntu1 [1130 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main armhf mount armhf 2.37.2-4ubuntu1 [125 kB] Get:55 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf systemd armhf 249.5-2ubuntu1 [4440 kB] Get:56 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsystemd0 armhf 249.5-2ubuntu1 [296 kB] Get:57 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libudev1 armhf 249.5-2ubuntu1 [70.7 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main armhf libapt-pkg6.0 armhf 2.3.13 [899 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main armhf dpkg armhf 1.20.9ubuntu3 [1215 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main armhf dash armhf 0.5.11+git20210903+057cd650a4ed-3 [83.8 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main armhf grep armhf 3.7-1 [150 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main armhf libncurses6 armhf 6.3-1 [87.5 kB] Get:63 http://ftpmaster.internal/ubuntu jammy/main armhf libncursesw6 armhf 6.3-1 [118 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main armhf libtinfo6 armhf 6.3-1 [88.2 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-bin armhf 6.3-1 [175 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main armhf ncurses-base all 6.3-1 [19.9 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main armhf gpgv armhf 2.2.27-2ubuntu1 [185 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main armhf apt armhf 2.3.13 [1378 kB] Get:69 http://ftpmaster.internal/ubuntu jammy/main armhf libsepol2 armhf 3.3-1 [263 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsemanage-common all 3.3-1build1 [10.0 kB] Get:71 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsemanage2 armhf 3.3-1build1 [84.1 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/main armhf passwd armhf 1:4.8.1-2ubuntu1 [740 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules-bin armhf 1.4.0-10ubuntu2 [35.6 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-modules armhf 1.4.0-10ubuntu2 [263 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main armhf logsave armhf 1.46.4-1ubuntu1 [10.3 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main armhf libext2fs2 armhf 1.46.4-1ubuntu1 [192 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main armhf e2fsprogs armhf 1.46.4-1ubuntu1 [565 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main armhf libattr1 armhf 1:2.5.1-1 [12.2 kB] Get:79 http://ftpmaster.internal/ubuntu jammy/main armhf libcom-err2 armhf 1.46.4-1ubuntu1 [9224 B] Get:80 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libk5crypto3 armhf 1.19.2-0ubuntu1 [83.6 kB] Get:81 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libkrb5support0 armhf 1.19.2-0ubuntu1 [30.5 kB] Get:82 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libkrb5-3 armhf 1.19.2-0ubuntu1 [330 kB] Get:83 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libgssapi-krb5-2 armhf 1.19.2-0ubuntu1 [120 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main armhf libpam-runtime all 1.4.0-10ubuntu2 [40.2 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/main armhf libsmartcols1 armhf 2.37.2-4ubuntu1 [93.7 kB] Get:86 http://ftpmaster.internal/ubuntu jammy/main armhf libss2 armhf 1.46.4-1ubuntu1 [10.1 kB] Get:87 http://ftpmaster.internal/ubuntu jammy/main armhf sensible-utils all 0.0.17 [20.1 kB] Get:88 http://ftpmaster.internal/ubuntu jammy/main armhf usrmerge all 25ubuntu2 [54.7 kB] Get:89 http://ftpmaster.internal/ubuntu jammy/main armhf openssl armhf 3.0.0-1ubuntu1 [1148 kB] Get:90 http://ftpmaster.internal/ubuntu jammy/main armhf ca-certificates all 20211016 [148 kB] Get:91 http://ftpmaster.internal/ubuntu jammy/main armhf libsqlite3-0 armhf 3.36.0-2 [571 kB] 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armhf linux-libc-dev armhf 5.15.0-13.13 [1235 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main armhf lockfile-progs armhf 0.1.19 [9508 B] Get:104 http://ftpmaster.internal/ubuntu jammy/main armhf pkgbinarymangler all 149 [32.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 69.3 MB in 8s (8436 kB/s) (Reading database ... 12985 files and directories currently installed.) 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Setting up libss2:armhf (1.46.4-1ubuntu1) ... Setting up libncursesw6:armhf (6.3-1) ... Setting up libdpkg-perl (1.20.9ubuntu3) ... Setting up logsave (1.46.4-1ubuntu1) ... Setting up libubsan1:armhf (11.2.0-12ubuntu1) ... Setting up libgcc-11-dev:armhf (11.2.0-12ubuntu1) ... Setting up mount (2.37.2-4ubuntu1) ... Setting up sensible-utils (0.0.17) ... Setting up libcrypt-dev:armhf (1:4.4.26-1) ... Setting up gpgconf (2.2.27-2ubuntu1) ... Setting up libcryptsetup12:armhf (2:2.4.2-1ubuntu3) ... Setting up libbinutils:armhf (2.37-10ubuntu1) ... Setting up libisl23:armhf (0.24-2) ... Setting up openssl (3.0.0-1ubuntu1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libcc1-0:armhf (11.2.0-12ubuntu1) ... Setting up gpg (2.2.27-2ubuntu1) ... Setting up libkmod2:armhf (28-1ubuntu5) ... Setting up libgdbm6:armhf (1.22-1) ... Setting up libctf0:armhf (2.37-10ubuntu1) ... Setting up cpp-11 (11.2.0-12ubuntu1) ... Setting up gpg-agent (2.2.27-2ubuntu1) ... Setting up pkgbinarymangler (149) ... Setting up e2fsprogs (1.46.4-1ubuntu1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up systemd (249.5-2ubuntu1) ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/resolved.conf ... Initializing machine ID from random generator. Setting up ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 7 added, 8 removed; done. Setting up systemd-timesyncd (249.5-2ubuntu1) ... Setting up libgdbm-compat4:armhf (1.22-1) ... Setting up libstdc++-11-dev:armhf (11.2.0-12ubuntu1) ... Setting up binutils-arm-linux-gnueabihf (2.37-10ubuntu1) ... Setting up systemd-sysv (249.5-2ubuntu1) ... Setting up binutils (2.37-10ubuntu1) ... Setting up dpkg-dev (1.20.9ubuntu3) ... Setting up gcc-11 (11.2.0-12ubuntu1) ... Setting up g++-11 (11.2.0-12ubuntu1) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... Processing triggers for ca-certificates (20211016) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-22599315 armhf jammy-proposed -c chroot:build-PACKAGEBUILD-22599315 --arch=armhf --dist=jammy-proposed --nolog augustus_3.4.0+dfsg2-3build1.dsc Initiating build PACKAGEBUILD-22599315 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:52 UTC 2021 armv7l sbuild (Debian sbuild) 0.75.0 (21 Mar 2018) on bos02-arm64-059.buildd +==============================================================================+ | augustus 3.4.0+dfsg2-3build1 (armhf) Tue, 07 Dec 2021 17:37:37 +0000 | +==============================================================================+ Package: augustus Version: 3.4.0+dfsg2-3build1 Source Version: 3.4.0+dfsg2-3build1 Distribution: jammy-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf Build Type: any I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-22599315/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- augustus_3.4.0+dfsg2-3build1.dsc exists in .; copying to chroot I: NOTICE: Log filtering will replace 'build/augustus-j12tW4/augustus-3.4.0+dfsg2' with '<>' I: NOTICE: Log filtering will replace 'build/augustus-j12tW4' with '<>' +------------------------------------------------------------------------------+ | Install build-essential | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-hFZW5d/apt_archive/sbuild-build-depends-core-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 1 entries to output Packages file. Ign:1 copy:/<>/resolver-hFZW5d/apt_archive ./ InRelease Get:2 copy:/<>/resolver-hFZW5d/apt_archive ./ Release [957 B] Ign:3 copy:/<>/resolver-hFZW5d/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-hFZW5d/apt_archive ./ Sources [349 B] Get:5 copy:/<>/resolver-hFZW5d/apt_archive ./ Packages [431 B] Fetched 1737 B in 0s (53.8 kB/s) Reading package lists... Reading package lists... Install core build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: systemd-timesyncd Use 'apt autoremove' to remove it. The following NEW packages will be installed: sbuild-build-depends-core-dummy 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 652 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-hFZW5d/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [652 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 652 B in 0s (48.0 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 13179 files and directories currently installed.) Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ... Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ... Setting up sbuild-build-depends-core-dummy (0.invalid.0) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armhf included in any all) +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools Filtered Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libboost-serialization-dev, libssl-dev, libmysql++-dev, asciidoctor, python3, samtools dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<>/resolver-hFZW5d/apt_archive/sbuild-build-depends-augustus-dummy.deb'. dpkg-scanpackages: warning: Packages in archive but missing from override file: dpkg-scanpackages: warning: sbuild-build-depends-augustus-dummy sbuild-build-depends-core-dummy dpkg-scanpackages: info: Wrote 2 entries to output Packages file. Ign:1 copy:/<>/resolver-hFZW5d/apt_archive ./ InRelease Get:2 copy:/<>/resolver-hFZW5d/apt_archive ./ Release [963 B] Ign:3 copy:/<>/resolver-hFZW5d/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-hFZW5d/apt_archive ./ Sources [600 B] Get:5 copy:/<>/resolver-hFZW5d/apt_archive ./ Packages [683 B] Fetched 2246 B in 0s (67.8 kB/s) Reading package lists... Reading package lists... Install augustus build dependencies (apt-based resolver) -------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: systemd-timesyncd Use 'apt autoremove' to remove it. The following additional packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit default-libmysqlclient-dev dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization-dev libboost-serialization1.74-dev libboost-serialization1.74.0 libboost1.74-dev libbrotli1 libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3 libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu67 libklu1 liblapack-dev liblapack3 libldap-2.5-0 libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmd0 libmetis5 libmongoose2 libmpdec3 libmysql++-dev libmysql++3v5 libmysqlclient-dev libmysqlclient21 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librbio2 librtmp1 libruby3.0 libsasl2-2 libsasl2-modules-db libsigsegv2 libsliplu1 libspqr2 libsqlite3-dev libssh-4 libssl-dev libsub-override-perl libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5 libxml2 libyaml-0-2 libzstd-dev lzma-dev m4 man-db media-types mysql-common po-debconf python3 python3-minimal python3.9 python3.9-minimal rake ruby ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert ruby-rubygems ruby-test-unit ruby-xmlrpc ruby3.0 rubygems-integration samtools zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libbamtools-doc liblapack-doc libboost1.74-doc libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-python1.74-dev libboost-random1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html icu-doc liblzma-doc libmysql++-doc ncurses-doc sqlite3-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv python3.9-doc binfmt-support ri ruby-dev bundler cwltool Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libldap-common publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl zip fonts-lato libjs-jquery The following NEW packages will be installed: asciidoctor autoconf automake autopoint autotools-dev bsdextrautils debhelper debugedit default-libmysqlclient-dev dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base icu-devtools intltool-debian libamd2 libarchive-zip-perl libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev libboost-iostreams1.74-dev libboost-iostreams1.74.0 libboost-regex1.74-dev libboost-regex1.74.0 libboost-serialization-dev libboost-serialization1.74-dev libboost-serialization1.74.0 libboost1.74-dev libbrotli1 libbsd0 libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3 libdebhelper-perl libdeflate-dev libdeflate0 libdw1 libedit2 libelf1 libexpat1 libfile-stripnondeterminism-perl libgfortran5 libgsl-dev libgsl27 libgslcblas0 libhts-dev libhts3 libhtscodecs2 libicu-dev libicu67 libklu1 liblapack-dev liblapack3 libldap-2.5-0 libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmd0 libmetis5 libmongoose2 libmpdec3 libmysql++-dev libmysql++3v5 libmysqlclient-dev libmysqlclient21 libncurses-dev libncurses5-dev libnghttp2-14 libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librbio2 librtmp1 libruby3.0 libsasl2-2 libsasl2-modules-db libsigsegv2 libsliplu1 libspqr2 libsqlite3-dev libssh-4 libssl-dev libsub-override-perl libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5 libxml2 libyaml-0-2 libzstd-dev lzma-dev m4 man-db media-types mysql-common po-debconf python3 python3-minimal python3.9 python3.9-minimal rake ruby ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert ruby-rubygems ruby-test-unit ruby-xmlrpc ruby3.0 rubygems-integration samtools sbuild-build-depends-augustus-dummy zlib1g-dev 0 upgraded, 130 newly installed, 0 to remove and 0 not upgraded. Need to get 73.1 MB of archives. After this operation, 379 MB of additional disk space will be used. Get:1 copy:/<>/resolver-hFZW5d/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [766 B] Get:2 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.9-minimal armhf 3.9.9-1build1 [776 kB] Get:3 http://ftpmaster.internal/ubuntu jammy/main armhf libexpat1 armhf 2.4.1-3 [64.9 kB] Get:4 http://ftpmaster.internal/ubuntu jammy/main armhf python3.9-minimal armhf 3.9.9-1build1 [1753 kB] Get:5 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf python3-minimal armhf 3.9.7-4 [24.7 kB] Get:6 http://ftpmaster.internal/ubuntu jammy/main armhf media-types all 4.0.0 [22.2 kB] Get:7 http://ftpmaster.internal/ubuntu jammy/main armhf libmpdec3 armhf 2.5.1-2build1 [76.5 kB] Get:8 http://ftpmaster.internal/ubuntu jammy/main armhf libpython3.9-stdlib armhf 3.9.9-1build1 [1731 kB] Get:9 http://ftpmaster.internal/ubuntu jammy/main armhf python3.9 armhf 3.9.9-1build1 [437 kB] Get:10 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libpython3-stdlib armhf 3.9.7-4 [7298 B] Get:11 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf python3 armhf 3.9.7-4 [22.8 kB] Get:12 http://ftpmaster.internal/ubuntu jammy/main armhf bsdextrautils armhf 2.37.2-4ubuntu1 [77.1 kB] Get:13 http://ftpmaster.internal/ubuntu jammy/main armhf libuchardet0 armhf 0.0.7-1build1 [75.6 kB] Get:14 http://ftpmaster.internal/ubuntu jammy/main armhf groff-base armhf 1.22.4-7 [870 kB] Get:15 http://ftpmaster.internal/ubuntu jammy/main armhf libpipeline1 armhf 1.5.4-1 [25.2 kB] Get:16 http://ftpmaster.internal/ubuntu jammy/main armhf man-db armhf 2.9.4-2build1 [1143 kB] Get:17 http://ftpmaster.internal/ubuntu jammy/main armhf libmd0 armhf 1.0.4-1 [22.5 kB] Get:18 http://ftpmaster.internal/ubuntu jammy/main armhf libbsd0 armhf 0.11.3-1ubuntu3 [39.6 kB] Get:19 http://ftpmaster.internal/ubuntu jammy/main armhf libelf1 armhf 0.186-1 [43.2 kB] Get:20 http://ftpmaster.internal/ubuntu jammy/main armhf libicu67 armhf 67.1-7ubuntu1 [9788 kB] Get:21 http://ftpmaster.internal/ubuntu jammy/main armhf libxml2 armhf 2.9.12+dfsg-5 [598 kB] Get:22 http://ftpmaster.internal/ubuntu jammy/main armhf libyaml-0-2 armhf 0.2.2-1build1 [45.4 kB] Get:23 http://ftpmaster.internal/ubuntu jammy/main armhf libmagic-mgc armhf 1:5.41-2 [257 kB] Get:24 http://ftpmaster.internal/ubuntu jammy/main armhf libmagic1 armhf 1:5.41-2 [80.2 kB] Get:25 http://ftpmaster.internal/ubuntu jammy/main armhf file armhf 1:5.41-2 [20.6 kB] Get:26 http://ftpmaster.internal/ubuntu jammy/main armhf gettext-base armhf 0.21-4ubuntu3 [36.0 kB] Get:27 http://ftpmaster.internal/ubuntu jammy/main armhf libedit2 armhf 3.1-20210910-1 [78.5 kB] Get:28 http://ftpmaster.internal/ubuntu jammy/main armhf libpsl5 armhf 0.21.0-1.2build1 [56.1 kB] Get:29 http://ftpmaster.internal/ubuntu jammy/main armhf rubygems-integration all 1.18 [5336 B] Get:30 http://ftpmaster.internal/ubuntu jammy/main armhf rake all 13.0.3-1 [61.5 kB] Get:31 http://ftpmaster.internal/ubuntu jammy/main armhf ruby-minitest all 5.13.0-1 [40.9 kB] Get:32 http://ftpmaster.internal/ubuntu jammy/main armhf ruby-net-telnet all 0.1.1-2 [12.6 kB] Get:33 http://ftpmaster.internal/ubuntu jammy/main armhf ruby-power-assert all 1.1.7-2 [11.5 kB] Get:34 http://ftpmaster.internal/ubuntu jammy/main armhf ruby-test-unit all 3.3.9-1 [73.6 kB] Get:35 http://ftpmaster.internal/ubuntu jammy/main armhf ruby-xmlrpc all 0.3.2-1 [24.6 kB] Get:36 http://ftpmaster.internal/ubuntu jammy/universe armhf libruby3.0 armhf 3.0.2-5ubuntu1 [4906 kB] Get:37 http://ftpmaster.internal/ubuntu jammy/universe armhf ruby3.0 armhf 3.0.2-5ubuntu1 [50.0 kB] Get:38 http://ftpmaster.internal/ubuntu jammy/main armhf ruby-rubygems all 3.2.27-3 [214 kB] Get:39 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf ruby armhf 1:3.0~exp1 [5100 B] Get:40 http://ftpmaster.internal/ubuntu jammy/universe armhf ruby-asciidoctor all 2.0.16-2 [173 kB] Get:41 http://ftpmaster.internal/ubuntu jammy/universe armhf asciidoctor all 2.0.16-2 [44.3 kB] Get:42 http://ftpmaster.internal/ubuntu jammy/main armhf libsigsegv2 armhf 2.13-1ubuntu2 [13.7 kB] Get:43 http://ftpmaster.internal/ubuntu jammy/main armhf m4 armhf 1.4.18-5ubuntu1 [192 kB] Get:44 http://ftpmaster.internal/ubuntu jammy/main armhf autoconf all 2.71-2 [338 kB] Get:45 http://ftpmaster.internal/ubuntu jammy/main armhf autotools-dev all 20180224.1+nmu1 [39.4 kB] Get:46 http://ftpmaster.internal/ubuntu jammy/main armhf automake all 1:1.16.5-1.1 [558 kB] Get:47 http://ftpmaster.internal/ubuntu jammy/main armhf autopoint all 0.21-4ubuntu3 [422 kB] Get:48 http://ftpmaster.internal/ubuntu jammy/main armhf libdebhelper-perl all 13.5.2ubuntu1 [66.0 kB] Get:49 http://ftpmaster.internal/ubuntu jammy/main armhf libtool all 2.4.6-15build1 [164 kB] Get:50 http://ftpmaster.internal/ubuntu jammy/main armhf dh-autoreconf all 20 [16.1 kB] Get:51 http://ftpmaster.internal/ubuntu jammy/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:52 http://ftpmaster.internal/ubuntu jammy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:53 http://ftpmaster.internal/ubuntu jammy/main armhf libfile-stripnondeterminism-perl all 1.12.1-1 [18.1 kB] Get:54 http://ftpmaster.internal/ubuntu jammy/main armhf dh-strip-nondeterminism all 1.12.1-1 [5200 B] Get:55 http://ftpmaster.internal/ubuntu jammy/main armhf libdw1 armhf 0.186-1 [228 kB] Get:56 http://ftpmaster.internal/ubuntu jammy/main armhf debugedit armhf 1:5.0-3 [43.2 kB] Get:57 http://ftpmaster.internal/ubuntu jammy/main armhf dwz armhf 0.14-1build1 [99.2 kB] Get:58 http://ftpmaster.internal/ubuntu jammy/main armhf gettext armhf 0.21-4ubuntu3 [755 kB] Get:59 http://ftpmaster.internal/ubuntu jammy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:60 http://ftpmaster.internal/ubuntu jammy/main armhf po-debconf all 1.0.21+nmu1 [233 kB] Get:61 http://ftpmaster.internal/ubuntu jammy/main armhf debhelper all 13.5.2ubuntu1 [926 kB] Get:62 http://ftpmaster.internal/ubuntu jammy/main armhf mysql-common all 5.8+1.0.7 [7498 B] Get:63 http://ftpmaster.internal/ubuntu jammy/main armhf libmysqlclient21 armhf 8.0.27-0ubuntu0.21.10.1 [1273 kB] Get:64 http://ftpmaster.internal/ubuntu jammy/main armhf libssl-dev armhf 3.0.0-1ubuntu1 [2074 kB] Get:65 http://ftpmaster.internal/ubuntu jammy/main armhf libzstd-dev armhf 1.4.8+dfsg-3 [353 kB] Get:66 http://ftpmaster.internal/ubuntu jammy/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2ubuntu7 [157 kB] Get:67 http://ftpmaster.internal/ubuntu jammy/main armhf libmysqlclient-dev armhf 8.0.27-0ubuntu0.21.10.1 [1627 kB] Get:68 http://ftpmaster.internal/ubuntu jammy/main armhf default-libmysqlclient-dev armhf 1.0.7 [3888 B] Get:69 http://ftpmaster.internal/ubuntu jammy/main armhf icu-devtools armhf 67.1-7ubuntu1 [183 kB] Get:70 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsuitesparseconfig5 armhf 1:5.10.1+dfsg-3 [10.1 kB] Get:71 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libamd2 armhf 1:5.10.1+dfsg-3 [15.0 kB] Get:72 http://ftpmaster.internal/ubuntu jammy/universe armhf libbamtools2.5.1 armhf 2.5.1+dfsg-10 [155 kB] Get:73 http://ftpmaster.internal/ubuntu jammy/universe armhf libbamtools-dev armhf 2.5.1+dfsg-10 [216 kB] Get:74 http://ftpmaster.internal/ubuntu jammy/main armhf libblas3 armhf 3.9.0-3ubuntu3 [113 kB] Get:75 http://ftpmaster.internal/ubuntu jammy/main armhf libblas-dev armhf 3.9.0-3ubuntu3 [120 kB] Get:76 http://ftpmaster.internal/ubuntu jammy/main armhf libboost1.74-dev armhf 1.74.0-13ubuntu1 [9619 kB] Get:77 http://ftpmaster.internal/ubuntu jammy/main armhf libboost-regex1.74.0 armhf 1.74.0-13ubuntu1 [470 kB] Get:78 http://ftpmaster.internal/ubuntu jammy/main armhf libicu-dev armhf 67.1-7ubuntu1 [10.8 MB] Get:79 http://ftpmaster.internal/ubuntu jammy/main armhf libboost-regex1.74-dev armhf 1.74.0-13ubuntu1 [598 kB] Get:80 http://ftpmaster.internal/ubuntu jammy/main armhf libboost-iostreams1.74.0 armhf 1.74.0-13ubuntu1 [241 kB] Get:81 http://ftpmaster.internal/ubuntu jammy/universe armhf libboost-iostreams1.74-dev armhf 1.74.0-13ubuntu1 [251 kB] Get:82 http://ftpmaster.internal/ubuntu jammy/universe armhf libboost-iostreams-dev armhf 1.74.0.3ubuntu6 [3196 B] Get:83 http://ftpmaster.internal/ubuntu jammy/main armhf libboost-serialization1.74.0 armhf 1.74.0-13ubuntu1 [313 kB] Get:84 http://ftpmaster.internal/ubuntu jammy/main armhf libboost-serialization1.74-dev armhf 1.74.0-13ubuntu1 [389 kB] Get:85 http://ftpmaster.internal/ubuntu jammy/universe armhf libboost-serialization-dev armhf 1.74.0.3ubuntu6 [3416 B] Get:86 http://ftpmaster.internal/ubuntu jammy/main armhf libbrotli1 armhf 1.0.9-2build4 [306 kB] Get:87 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libbtf1 armhf 1:5.10.1+dfsg-3 [10.3 kB] Get:88 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libbz2-dev armhf 1.0.8-5 [29.8 kB] Get:89 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libcamd2 armhf 1:5.10.1+dfsg-3 [15.5 kB] Get:90 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libccolamd2 armhf 1:5.10.1+dfsg-3 [16.7 kB] Get:91 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libcolamd2 armhf 1:5.10.1+dfsg-3 [13.1 kB] Get:92 http://ftpmaster.internal/ubuntu jammy/main armhf libgfortran5 armhf 11.2.0-12ubuntu1 [287 kB] Get:93 http://ftpmaster.internal/ubuntu jammy/main armhf liblapack3 armhf 3.9.0-3ubuntu3 [1891 kB] Get:94 http://ftpmaster.internal/ubuntu jammy/main armhf libmetis5 armhf 5.1.0.dfsg-7build1 [144 kB] Get:95 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libcholmod3 armhf 1:5.10.1+dfsg-3 [233 kB] Get:96 http://ftpmaster.internal/ubuntu jammy/main armhf libsasl2-modules-db armhf 2.1.27+dfsg2-2build1 [19.1 kB] Get:97 http://ftpmaster.internal/ubuntu jammy/main armhf libsasl2-2 armhf 2.1.27+dfsg2-2build1 [50.7 kB] Get:98 http://ftpmaster.internal/ubuntu jammy/main armhf libldap-2.5-0 armhf 2.5.6+dfsg-1~exp1ubuntu1 [162 kB] Get:99 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libnghttp2-14 armhf 1.43.0-1build2 [70.1 kB] Get:100 http://ftpmaster.internal/ubuntu jammy/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2build3 [53.0 kB] Get:101 http://ftpmaster.internal/ubuntu jammy/main armhf libssh-4 armhf 0.9.6-1build1 [163 kB] Get:102 http://ftpmaster.internal/ubuntu jammy/main armhf libcurl3-gnutls armhf 7.74.0-1.3ubuntu2 [234 kB] Get:103 http://ftpmaster.internal/ubuntu jammy/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3ubuntu2 [337 kB] Get:104 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libcxsparse3 armhf 1:5.10.1+dfsg-3 [40.1 kB] Get:105 http://ftpmaster.internal/ubuntu jammy/main armhf libdeflate0 armhf 1.8-1ubuntu1 [46.1 kB] Get:106 http://ftpmaster.internal/ubuntu jammy/main armhf libdeflate-dev armhf 1.8-1ubuntu1 [40.4 kB] Get:107 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf libgslcblas0 armhf 2.7.1+dfsg-3 [73.7 kB] Get:108 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf libgsl27 armhf 2.7.1+dfsg-3 [842 kB] Get:109 http://ftpmaster.internal/ubuntu jammy-proposed/universe armhf libgsl-dev armhf 2.7.1+dfsg-3 [1080 kB] Get:110 http://ftpmaster.internal/ubuntu jammy/universe armhf libhtscodecs2 armhf 1.1.1-3 [53.6 kB] Get:111 http://ftpmaster.internal/ubuntu jammy/universe armhf libhts3 armhf 1.13+ds-2 [346 kB] Get:112 http://ftpmaster.internal/ubuntu jammy/main armhf liblzma-dev armhf 5.2.5-2build1 [149 kB] Get:113 http://ftpmaster.internal/ubuntu jammy/universe armhf libhts-dev armhf 1.13+ds-2 [4037 kB] Get:114 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libklu1 armhf 1:5.10.1+dfsg-3 [39.7 kB] Get:115 http://ftpmaster.internal/ubuntu jammy/main armhf liblapack-dev armhf 3.9.0-3ubuntu3 [1960 kB] Get:116 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libldl2 armhf 1:5.10.1+dfsg-3 [10.1 kB] Get:117 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libmongoose2 armhf 1:5.10.1+dfsg-3 [30.2 kB] Get:118 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libumfpack5 armhf 1:5.10.1+dfsg-3 [131 kB] Get:119 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf librbio2 armhf 1:5.10.1+dfsg-3 [18.7 kB] Get:120 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libspqr2 armhf 1:5.10.1+dfsg-3 [59.6 kB] Get:121 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsliplu1 armhf 1:5.10.1+dfsg-3 [36.9 kB] Get:122 http://ftpmaster.internal/ubuntu jammy-proposed/main armhf libsuitesparse-dev armhf 1:5.10.1+dfsg-3 [709 kB] Get:123 http://ftpmaster.internal/ubuntu jammy/main armhf liblpsolve55-dev armhf 5.5.2.5-2build1 [405 kB] Get:124 http://ftpmaster.internal/ubuntu jammy/universe armhf libmysql++3v5 armhf 3.2.5-2.1 [105 kB] Get:125 http://ftpmaster.internal/ubuntu jammy/universe armhf libmysql++-dev armhf 3.2.5-2.1 [96.4 kB] Get:126 http://ftpmaster.internal/ubuntu jammy/main armhf libncurses-dev armhf 6.3-1 [342 kB] Get:127 http://ftpmaster.internal/ubuntu jammy/main armhf libncurses5-dev armhf 6.3-1 [780 B] Get:128 http://ftpmaster.internal/ubuntu jammy/main armhf libsqlite3-dev armhf 3.36.0-2 [758 kB] Get:129 http://ftpmaster.internal/ubuntu jammy/universe armhf lzma-dev all 9.22-2.2 [41.6 kB] Get:130 http://ftpmaster.internal/ubuntu jammy/universe armhf samtools armhf 1.13-4 [538 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 73.1 MB in 9s (8272 kB/s) Selecting previously unselected package libpython3.9-minimal:armhf. 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Unpacking libsuitesparse-dev:armhf (1:5.10.1+dfsg-3) ... Selecting previously unselected package liblpsolve55-dev. Preparing to unpack .../112-liblpsolve55-dev_5.5.2.5-2build1_armhf.deb ... Unpacking liblpsolve55-dev (5.5.2.5-2build1) ... Selecting previously unselected package libmysql++3v5:armhf. Preparing to unpack .../113-libmysql++3v5_3.2.5-2.1_armhf.deb ... Unpacking libmysql++3v5:armhf (3.2.5-2.1) ... Selecting previously unselected package libmysql++-dev:armhf. Preparing to unpack .../114-libmysql++-dev_3.2.5-2.1_armhf.deb ... Unpacking libmysql++-dev:armhf (3.2.5-2.1) ... Selecting previously unselected package libncurses-dev:armhf. Preparing to unpack .../115-libncurses-dev_6.3-1_armhf.deb ... Unpacking libncurses-dev:armhf (6.3-1) ... Selecting previously unselected package libncurses5-dev:armhf. Preparing to unpack .../116-libncurses5-dev_6.3-1_armhf.deb ... Unpacking libncurses5-dev:armhf (6.3-1) ... Selecting previously unselected package libsqlite3-dev:armhf. 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Setting up libncurses-dev:armhf (6.3-1) ... Setting up libpsl5:armhf (0.21.0-1.2build1) ... Setting up libboost1.74-dev:armhf (1.74.0-13ubuntu1) ... Setting up libzstd-dev:armhf (1.4.8+dfsg-3) ... Setting up bsdextrautils (2.37.2-4ubuntu1) ... update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode Setting up libicu67:armhf (67.1-7ubuntu1) ... Setting up libgslcblas0:armhf (2.7.1+dfsg-3) ... Setting up ruby-power-assert (1.1.7-2) ... Setting up libmagic-mgc (1:5.41-2) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:armhf (0.2.2-1build1) ... Setting up libboost-iostreams1.74.0:armhf (1.74.0-13ubuntu1) ... Setting up libdebhelper-perl (13.5.2ubuntu1) ... Setting up libbrotli1:armhf (1.0.9-2build4) ... Setting up libldl2:armhf (1:5.10.1+dfsg-3) ... Setting up libnghttp2-14:armhf (1.43.0-1build2) ... Setting up libmagic1:armhf (1:5.41-2) ... Setting up libdeflate0:armhf (1.8-1ubuntu1) ... Setting up gettext-base (0.21-4ubuntu3) ... Setting up libgsl27:armhf (2.7.1+dfsg-3) ... Setting up rubygems-integration (1.18) ... Setting up libmetis5:armhf (5.1.0.dfsg-7build1) ... Setting up file (1:5.41-2) ... Setting up libbtf1:armhf (1:5.10.1+dfsg-3) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg2-2build1) ... Setting up ruby-minitest (5.13.0-1) ... Setting up autotools-dev (20180224.1+nmu1) ... Setting up libblas3:armhf (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libsqlite3-dev:armhf (3.36.0-2) ... Setting up ruby-test-unit (3.3.9-1) ... Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2build3) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libsigsegv2:armhf (2.13-1ubuntu2) ... Setting up libboost-regex1.74.0:armhf (1.74.0-13ubuntu1) ... Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-10) ... Setting up libssl-dev:armhf (3.0.0-1ubuntu1) ... Setting up autopoint (0.21-4ubuntu3) ... Setting up icu-devtools (67.1-7ubuntu1) ... Setting up libmysql++3v5:armhf (3.2.5-2.1) ... Setting up libsasl2-2:armhf (2.1.27+dfsg2-2build1) ... Setting up libssh-4:armhf (0.9.6-1build1) ... Setting up libgfortran5:armhf (11.2.0-12ubuntu1) ... Setting up liblzma-dev:armhf (5.2.5-2build1) ... Setting up libboost-serialization1.74.0:armhf (1.74.0-13ubuntu1) ... Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2ubuntu7) ... Setting up libmd0:armhf (1.0.4-1) ... Setting up libuchardet0:armhf (0.0.7-1build1) ... Setting up libncurses5-dev:armhf (6.3-1) ... Setting up libmpdec3:armhf (2.5.1-2build1) ... Setting up libsub-override-perl (0.09-2) ... Setting up libcxsparse3:armhf (1:5.10.1+dfsg-3) ... Setting up libbsd0:armhf (0.11.3-1ubuntu3) ... Setting up libdeflate-dev:armhf (1.8-1ubuntu1) ... Setting up libelf1:armhf (0.186-1) ... Setting up libicu-dev:armhf (67.1-7ubuntu1) ... Setting up ruby-xmlrpc (0.3.2-1) ... Setting up libxml2:armhf (2.9.12+dfsg-5) ... Setting up libsuitesparseconfig5:armhf (1:5.10.1+dfsg-3) ... Setting up libblas-dev:armhf (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode Setting up libmysqlclient-dev (8.0.27-0ubuntu0.21.10.1) ... Setting up librbio2:armhf (1:5.10.1+dfsg-3) ... Setting up libpython3.9-stdlib:armhf (3.9.9-1build1) ... Setting up libpython3-stdlib:armhf (3.9.7-4) ... Setting up libbz2-dev:armhf (1.0.8-5) ... Setting up default-libmysqlclient-dev:armhf (1.0.7) ... Setting up libfile-stripnondeterminism-perl (1.12.1-1) ... Setting up libamd2:armhf (1:5.10.1+dfsg-3) ... Setting up libdw1:armhf (0.186-1) ... Setting up liblapack3:armhf (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.21-4ubuntu3) ... Setting up libgsl-dev (2.7.1+dfsg-3) ... Setting up libcolamd2:armhf (1:5.10.1+dfsg-3) ... Setting up libtool (2.4.6-15build1) ... Setting up libedit2:armhf (3.1-20210910-1) ... Setting up m4 (1.4.18-5ubuntu1) ... Setting up libldap-2.5-0:armhf (2.5.6+dfsg-1~exp1ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libmysql++-dev:armhf (3.2.5-2.1) ... Setting up libsliplu1:armhf (1:5.10.1+dfsg-3) ... Setting up libcamd2:armhf (1:5.10.1+dfsg-3) ... Setting up libmongoose2:armhf (1:5.10.1+dfsg-3) ... Setting up libbamtools-dev:armhf (2.5.1+dfsg-10) ... Setting up liblapack-dev:armhf (3.9.0-3ubuntu3) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode Setting up lzma-dev (9.22-2.2) ... Setting up autoconf (2.71-2) ... Setting up libboost-serialization1.74-dev:armhf (1.74.0-13ubuntu1) ... Setting up dh-strip-nondeterminism (1.12.1-1) ... Setting up dwz (0.14-1build1) ... Setting up libboost-regex1.74-dev:armhf (1.74.0-13ubuntu1) ... Setting up groff-base (1.22.4-7) ... Setting up libklu1:armhf (1:5.10.1+dfsg-3) ... Setting up libccolamd2:armhf (1:5.10.1+dfsg-3) ... Setting up debugedit (1:5.0-3) ... Setting up libcholmod3:armhf (1:5.10.1+dfsg-3) ... Setting up python3.9 (3.9.9-1build1) ... Setting up automake (1:1.16.5-1.1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libspqr2:armhf (1:5.10.1+dfsg-3) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libcurl3-gnutls:armhf (7.74.0-1.3ubuntu2) ... Setting up python3 (3.9.7-4) ... Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.3ubuntu2) ... Setting up man-db (2.9.4-2build1) ... Not building database; man-db/auto-update is not 'true'. Created symlink /etc/systemd/system/timers.target.wants/man-db.timer → /lib/systemd/system/man-db.timer. Setting up libboost-iostreams1.74-dev:armhf (1.74.0-13ubuntu1) ... Setting up dh-autoreconf (20) ... Setting up libumfpack5:armhf (1:5.10.1+dfsg-3) ... Setting up libboost-serialization-dev:armhf (1.74.0.3ubuntu6) ... Setting up libhts3:armhf (1.13+ds-2) ... Setting up libsuitesparse-dev:armhf (1:5.10.1+dfsg-3) ... Setting up libhts-dev:armhf (1.13+ds-2) ... Setting up debhelper (13.5.2ubuntu1) ... Setting up libboost-iostreams-dev:armhf (1.74.0.3ubuntu6) ... Setting up samtools (1.13-4) ... Setting up liblpsolve55-dev (5.5.2.5-2build1) ... Setting up ruby3.0 (3.0.2-5ubuntu1) ... Setting up ruby (1:3.0~exp1) ... Setting up ruby-asciidoctor (2.0.16-2) ... Setting up rake (13.0.3-1) ... Setting up asciidoctor (2.0.16-2) ... Setting up libruby3.0:armhf (3.0.2-5ubuntu1) ... Setting up ruby-rubygems (3.2.27-3) ... Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.34-0ubuntu3) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.15.0-163-generic arm64 (armv7l) Toolchain package versions: binutils_2.37-10ubuntu1 dpkg-dev_1.20.9ubuntu3 g++-11_11.2.0-12ubuntu1 gcc-11_11.2.0-12ubuntu1 libc6-dev_2.34-0ubuntu3 libstdc++-11-dev_11.2.0-12ubuntu1 libstdc++6_11.2.0-12ubuntu1 linux-libc-dev_5.15.0-13.13 Package versions: adduser_3.118ubuntu5 advancecomp_2.1-2.1ubuntu1 apt_2.3.13 asciidoctor_2.0.16-2 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4ubuntu3 autotools-dev_20180224.1+nmu1 base-files_12ubuntu2 base-passwd_3.5.52 bash_5.1-5ubuntu1 binutils_2.37-10ubuntu1 binutils-arm-linux-gnueabihf_2.37-10ubuntu1 binutils-common_2.37-10ubuntu1 bsdextrautils_2.37.2-4ubuntu1 bsdutils_1:2.37.2-4ubuntu1 build-essential_12.9ubuntu2 bzip2_1.0.8-5 ca-certificates_20211016 coreutils_8.32-4ubuntu3 cpp_4:11.2.0-1ubuntu1 cpp-11_11.2.0-12ubuntu1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2ubuntu1 debianutils_5.5-1ubuntu1 debugedit_1:5.0-3 default-libmysqlclient-dev_1.0.7 dh-autoreconf_20 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.8-0ubuntu1 dpkg_1.20.9ubuntu3 dpkg-dev_1.20.9ubuntu3 dwz_0.14-1build1 e2fsprogs_1.46.4-1ubuntu1 fakeroot_1.25.3-1.1ubuntu3 file_1:5.41-2 findutils_4.8.0-1ubuntu2 g++_4:11.2.0-1ubuntu1 g++-11_11.2.0-12ubuntu1 gcc_4:11.2.0-1ubuntu1 gcc-11_11.2.0-12ubuntu1 gcc-11-base_11.2.0-12ubuntu1 gettext_0.21-4ubuntu3 gettext-base_0.21-4ubuntu3 gpg_2.2.27-2ubuntu1 gpg-agent_2.2.27-2ubuntu1 gpgconf_2.2.27-2ubuntu1 gpgv_2.2.27-2ubuntu1 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4ubuntu2 hostname_3.23ubuntu1 icu-devtools_67.1-7ubuntu1 init_1.60build1 init-system-helpers_1.60build1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10ubuntu2 libamd2_1:5.10.1+dfsg-3 libapparmor1_3.0.3-0ubuntu4 libapt-pkg6.0_2.3.13 libarchive-zip-perl_1.68-1 libargon2-1_0~20171227-0.2build22 libasan6_11.2.0-12ubuntu1 libassuan0_2.5.5-1 libatomic1_11.2.0-12ubuntu1 libattr1_1:2.5.1-1 libaudit-common_1:3.0-2ubuntu3 libaudit1_1:3.0-2ubuntu3 libbamtools-dev_2.5.1+dfsg-10 libbamtools2.5.1_2.5.1+dfsg-10 libbinutils_2.37-10ubuntu1 libblas-dev_3.9.0-3ubuntu3 libblas3_3.9.0-3ubuntu3 libblkid1_2.37.2-4ubuntu1 libboost-iostreams-dev_1.74.0.3ubuntu6 libboost-iostreams1.74-dev_1.74.0-13ubuntu1 libboost-iostreams1.74.0_1.74.0-13ubuntu1 libboost-regex1.74-dev_1.74.0-13ubuntu1 libboost-regex1.74.0_1.74.0-13ubuntu1 libboost-serialization-dev_1.74.0.3ubuntu6 libboost-serialization1.74-dev_1.74.0-13ubuntu1 libboost-serialization1.74.0_1.74.0-13ubuntu1 libboost1.74-dev_1.74.0-13ubuntu1 libbrotli1_1.0.9-2build4 libbsd0_0.11.3-1ubuntu3 libbtf1_1:5.10.1+dfsg-3 libbz2-1.0_1.0.8-5 libbz2-dev_1.0.8-5 libc-bin_2.34-0ubuntu3 libc-dev-bin_2.34-0ubuntu3 libc6_2.34-0ubuntu3 libc6-dev_2.34-0ubuntu3 libcamd2_1:5.10.1+dfsg-3 libcap-ng0_0.7.9-2.2build2 libcap2_1:2.44-1build2 libcc1-0_11.2.0-12ubuntu1 libccolamd2_1:5.10.1+dfsg-3 libcholmod3_1:5.10.1+dfsg-3 libcolamd2_1:5.10.1+dfsg-3 libcom-err2_1.46.4-1ubuntu1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libcryptsetup12_2:2.4.2-1ubuntu3 libctf-nobfd0_2.37-10ubuntu1 libctf0_2.37-10ubuntu1 libcurl3-gnutls_7.74.0-1.3ubuntu2 libcurl4-gnutls-dev_7.74.0-1.3ubuntu2 libcxsparse3_1:5.10.1+dfsg-3 libdb5.3_5.3.28+dfsg1-0.8ubuntu2 libdebconfclient0_0.256ubuntu4 libdebhelper-perl_13.5.2ubuntu1 libdeflate-dev_1.8-1ubuntu1 libdeflate0_1.8-1ubuntu1 libdevmapper1.02.1_2:1.02.175-2.1ubuntu3 libdpkg-perl_1.20.9ubuntu3 libdw1_0.186-1 libedit2_3.1-20210910-1 libelf1_0.186-1 libexpat1_2.4.1-3 libext2fs2_1.46.4-1ubuntu1 libfakeroot_1.25.3-1.1ubuntu3 libffi8_3.4.2-1ubuntu5 libfile-stripnondeterminism-perl_1.12.1-1 libgcc-11-dev_11.2.0-12ubuntu1 libgcc-s1_11.2.0-12ubuntu1 libgcrypt20_1.9.4-3ubuntu2 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgfortran5_11.2.0-12ubuntu1 libgmp10_2:6.2.1+dfsg-1ubuntu3 libgnutls30_3.7.2-2ubuntu1 libgomp1_11.2.0-12ubuntu1 libgpg-error0_1.42-3 libgsl-dev_2.7.1+dfsg-3 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.19.2-0ubuntu1 libhogweed6_3.7.3-1build1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu-dev_67.1-7ubuntu1 libicu67_67.1-7ubuntu1 libidn2-0_2.3.2-2 libip4tc2_1.8.7-1ubuntu4 libisl23_0.24-2 libjson-c5_0.15-2build3 libk5crypto3_1.19.2-0ubuntu1 libkeyutils1_1.6.1-2ubuntu2 libklu1_1:5.10.1+dfsg-3 libkmod2_28-1ubuntu5 libkrb5-3_1.19.2-0ubuntu1 libkrb5support0_1.19.2-0ubuntu1 liblapack-dev_3.9.0-3ubuntu3 liblapack3_3.9.0-3ubuntu3 libldap-2.5-0_2.5.6+dfsg-1~exp1ubuntu1 libldl2_1:5.10.1+dfsg-3 liblockfile-bin_1.17-1build1 liblockfile1_1.17-1build1 liblpsolve55-dev_5.5.2.5-2build1 liblz4-1_1.9.3-2build1 liblzma-dev_5.2.5-2build1 liblzma5_5.2.5-2build1 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmd0_1.0.4-1 libmetis5_5.1.0.dfsg-7build1 libmongoose2_1:5.10.1+dfsg-3 libmount1_2.37.2-4ubuntu1 libmpc3_1.2.1-1 libmpdec3_2.5.1-2build1 libmpfr6_4.1.0-3build2 libmysql++-dev_3.2.5-2.1 libmysql++3v5_3.2.5-2.1 libmysqlclient-dev_8.0.27-0ubuntu0.21.10.1 libmysqlclient21_8.0.27-0ubuntu0.21.10.1 libncurses-dev_6.3-1 libncurses5-dev_6.3-1 libncurses6_6.3-1 libncursesw6_6.3-1 libnettle8_3.7.3-1build1 libnghttp2-14_1.43.0-1build2 libnpth0_1.6-3build1 libnsl-dev_1.3.0-2build1 libnsl2_1.3.0-2build1 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-10ubuntu2 libpam-modules-bin_1.4.0-10ubuntu2 libpam-runtime_1.4.0-10ubuntu2 libpam0g_1.4.0-10ubuntu2 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13build4 libperl5.32_5.32.1-3ubuntu3 libpipeline1_1.5.4-1 libpng16-16_1.6.37-3build4 libprocps8_2:3.3.17-5ubuntu3 libpsl5_0.21.0-1.2build1 libpython3-stdlib_3.9.7-4 libpython3.9-minimal_3.9.9-1build1 libpython3.9-stdlib_3.9.9-1build1 librbio2_1:5.10.1+dfsg-3 libreadline8_8.1-2build1 librtmp1_2.4+20151223.gitfa8646d.1-2build3 libruby3.0_3.0.2-5ubuntu1 libsasl2-2_2.1.27+dfsg2-2build1 libsasl2-modules-db_2.1.27+dfsg2-2build1 libseccomp2_2.5.2-2ubuntu2 libselinux1_3.3-1build1 libsemanage-common_3.3-1build1 libsemanage2_3.3-1build1 libsepol1_3.1-1ubuntu2 libsepol2_3.3-1 libsigsegv2_2.13-1ubuntu2 libsliplu1_1:5.10.1+dfsg-3 libsmartcols1_2.37.2-4ubuntu1 libspqr2_1:5.10.1+dfsg-3 libsqlite3-0_3.36.0-2 libsqlite3-dev_3.36.0-2 libss2_1.46.4-1ubuntu1 libssh-4_0.9.6-1build1 libssl-dev_3.0.0-1ubuntu1 libssl1.1_1.1.1l-1ubuntu1 libssl3_3.0.0-1ubuntu1 libstdc++-11-dev_11.2.0-12ubuntu1 libstdc++6_11.2.0-12ubuntu1 libsub-override-perl_0.09-2 libsuitesparse-dev_1:5.10.1+dfsg-3 libsuitesparseconfig5_1:5.10.1+dfsg-3 libsystemd0_249.5-2ubuntu1 libtasn1-6_4.18.0-4 libtinfo6_6.3-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15build1 libubsan1_11.2.0-12ubuntu1 libuchardet0_0.0.7-1build1 libudev1_249.5-2ubuntu1 libumfpack5_1:5.10.1+dfsg-3 libunistring2_0.9.10-6 libuuid1_2.37.2-4ubuntu1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2build1 libyaml-0-2_0.2.2-1build1 libzstd-dev_1.4.8+dfsg-3 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.15.0-13.13 lockfile-progs_0.1.19 login_1:4.8.1-2ubuntu1 logsave_1.46.4-1ubuntu1 lsb-base_11.1.0ubuntu3 lto-disabled-list_17 lzma-dev_9.22-2.2 m4_1.4.18-5ubuntu1 make_4.3-4ubuntu2 man-db_2.9.4-2build1 mawk_1.3.4.20200120-2build1 media-types_4.0.0 mount_2.37.2-4ubuntu1 mysql-common_5.8+1.0.7 ncurses-base_6.3-1 ncurses-bin_6.3-1 openssl_3.0.0-1ubuntu1 optipng_0.7.7-2 passwd_1:4.8.1-2ubuntu1 patch_2.7.6-7build1 perl_5.32.1-3ubuntu3 perl-base_5.32.1-3ubuntu3 perl-modules-5.32_5.32.1-3ubuntu3 pinentry-curses_1.1.1-1build1 pkgbinarymangler_149 po-debconf_1.0.21+nmu1 policyrcd-script-zg2_0.1-3 procps_2:3.3.17-5ubuntu3 python3_3.9.7-4 python3-minimal_3.9.7-4 python3.9_3.9.9-1build1 python3.9-minimal_3.9.9-1build1 rake_13.0.3-1 readline-common_8.1-2build1 rpcsvc-proto_1.4.2-0ubuntu5 ruby_1:3.0~exp1 ruby-asciidoctor_2.0.16-2 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-2 ruby-rubygems_3.2.27-3 ruby-test-unit_3.3.9-1 ruby-xmlrpc_0.3.2-1 ruby3.0_3.0.2-5ubuntu1 rubygems-integration_1.18 samtools_1.13-4 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1ubuntu2 sensible-utils_0.0.17 systemd_249.5-2ubuntu1 systemd-sysv_249.5-2ubuntu1 systemd-timesyncd_249.5-2ubuntu1 sysvinit-utils_2.96-7ubuntu2 tar_1.34+dfsg-1build2 tzdata_2021e-1ubuntu1 ubuntu-keyring_2021.03.26 usrmerge_25ubuntu2 util-linux_2.37.2-4ubuntu1 xz-utils_5.2.5-2build1 zlib1g_1:1.2.11.dfsg-2ubuntu7 zlib1g-dev_1:1.2.11.dfsg-2ubuntu7 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Tue Dec 7 17:24:35 2021 UTC gpgv: using RSA key AC483F68DE728F43F2202FCA568D30F321B2133D gpgv: issuer "steve.langasek@ubuntu.com" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./augustus_3.4.0+dfsg2-3build1.dsc dpkg-source: info: extracting augustus in /<>/augustus-3.4.0+dfsg2 dpkg-source: info: unpacking augustus_3.4.0+dfsg2.orig.tar.xz dpkg-source: info: unpacking augustus_3.4.0+dfsg2-3build1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying search_config_path dpkg-source: info: applying set_installdir dpkg-source: info: applying interpreter_paths.patch dpkg-source: info: applying switch_cgp_testing_off.patch dpkg-source: info: applying disable-compare.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf DEB_BUILD_OPTIONS=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-22599315 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-22599315 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-22599315 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package augustus dpkg-buildpackage: info: source version 3.4.0+dfsg2-3build1 dpkg-buildpackage: info: source distribution jammy dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean debian/rules override_dh_auto_clean make[1]: Entering directory '/<>/augustus-3.4.0+dfsg2' /usr/bin/make -C auxprogs/bam2hints clean make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2hints' rm -f bam2hints.o bam2hints ../../bin/bam2hints make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2hints' /usr/bin/make -C auxprogs/homGeneMapping clean make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping' cd src; make clean make[3]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' rm -f homGeneMapping gene.o genome.o sqliteDB.o rm -f ../../../bin/homGeneMapping make[3]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' cd ../..; tests/auxprogs/homGeneMapping/test_homGeneMapping.py --clean make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping' /usr/bin/make -C auxprogs/joingenes clean make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/joingenes' rm -rf *.o joingenes; rm -rf ../../bin/joingenes make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/joingenes' /usr/bin/make -C auxprogs/aln2wig clean make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/aln2wig' rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2wig clean make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2wig' rm -f bam2wig bam2wig.o bam2wig rm -f ../../bin/bam2wig cd ../..; tests/auxprogs/bam2wig/test_bam2wig.py --clean make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands clean make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam clean make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam' (cd src; make clean;) make[3]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o rm -f filterBam rm -f ../../../bin/filterBam make[3]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam' rm -rf bin rm -f debian/*substvars rm -f debian/mansrc/*.1 find . -name "__pycache__" | xargs -r rm -r find src -name "*.o" | xargs -r rm find auxprogs -name "*.o" | xargs -r rm rm -f auxprogs/utrrnaseq/Debug/utrrnaseq src/augustus src/etraining src/fastBlockSearch src/getSeq src/load2db src/load2sqlitedb src/pp_simScore src/prepareAlign make[1]: Leaving directory '/<>/augustus-3.4.0+dfsg2' dh_clean debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>/augustus-3.4.0+dfsg2' mkdir -p bin /usr/bin/make -C auxprogs/aln2wig make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/aln2wig' cc -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -c aln2wig.c In file included from /usr/include/string.h:519, from aln2wig.c:15: In function ‘strncpy’, inlined from ‘main’ at aln2wig.c:454:6: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘main’ at aln2wig.c:460:6: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘main’ at aln2wig.c:327:6: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘strncpy’, inlined from ‘main’ at aln2wig.c:334:6: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ cc -Wall -Wno-sign-compare -ansi -pedantic -O2 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o mkdir -p ../../bin cp aln2wig ../../bin make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/aln2wig' /usr/bin/make -C auxprogs/bam2hints make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2hints' g++ -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools g++ -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz mkdir -p ../../bin cp bam2hints ../../bin make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2hints' /usr/bin/make -C auxprogs/bam2wig make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2wig' cc -Wall -O2 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c bam2wig.c -o bam2wig.o -I/usr/include/htslib bam2wig.c: In function ‘main’: bam2wig.c:172:35: warning: format ‘%ld’ expects argument of type ‘long int’, but argument 2 has type ‘hts_pos_t’ {aka ‘long long int’} [-Wformat=] 172 | printf("%ld %d\n", pos+1, coverage); | ~~^ ~~~~~ | | | | long int hts_pos_t {aka long long int} | %lld cc -Wall -O2 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig -lhts -lz -lpthread mkdir -p ../../bin cp bam2wig ../../bin/bam2wig make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2wig' /usr/bin/make -C auxprogs/compileSpliceCands make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' cc -Wall -pedantic -ansi -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c compileSpliceCands.c: In function ‘getChromosome’: compileSpliceCands.c:226:9: warning: this decimal constant is unsigned only in ISO C90 226 | s = malloc(3500000000); | ^ In file included from /usr/include/string.h:519, from compileSpliceCands.c:12: In function ‘strncat’, inlined from ‘getChromosome’ at compileSpliceCands.c:216:2: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:135:10: warning: ‘__builtin_strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=] 135 | return __builtin___strncat_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 136 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c: In function ‘getChromosome’: compileSpliceCands.c:216:9: note: length computed here 216 | strncat(checkstring,chromosomename,strlen(chromosomename)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c:226:13: warning: argument 1 value ‘3500000000’ exceeds maximum object size 2147483647 [-Walloc-size-larger-than=] 226 | s = malloc(3500000000); | ^~~~~~~~~~~~~~~~~~ In file included from compileSpliceCands.c:14: /usr/include/stdlib.h:539:14: note: in a call to allocation function ‘malloc’ declared here 539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__ | ^~~~~~ In file included from /usr/include/string.h:519, from compileSpliceCands.c:12: In function ‘strncpy’, inlined from ‘parseLine’ at compileSpliceCands.c:292:2: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:10: warning: ‘__builtin_strncpy’ specified bound 256 equals destination size [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ compileSpliceCands.c: In function ‘parseList’: compileSpliceCands.c:350:85: warning: ‘left’ may be used uninitialized in this function [-Wmaybe-uninitialized] 350 | findPossibleSpliceSites(left->name,actualChromosome,left->startPos,left->endPos,right->startPos,right->endPos,left->strand,right->strand); | ~~~~^~~~~~ compileSpliceCands.c: In function ‘main’: compileSpliceCands.c:563:17: warning: ‘chromosomeLength’ may be used uninitialized in this function [-Wmaybe-uninitialized] 563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cc -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c cc -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o compileSpliceCands compileSpliceCands.o list.o cp compileSpliceCands ../../bin/compileSpliceCands make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' /usr/bin/make -C auxprogs/filterBam make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam' (cd src;make) make[3]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[3]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam' /usr/bin/make -C auxprogs/homGeneMapping/src make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o gene.o gene.cc -I../include g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o genome.o genome.cc -I../include g++ -c -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -o sqliteDB.o sqliteDB.cc -I../include g++ -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -O2 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DBOOST -DM_SQLITE -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o homGeneMapping main.cc gene.o genome.o sqliteDB.o -I../include -lsqlite3 mkdir -p ../../../bin/ cp homGeneMapping ../../../bin/homGeneMapping make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' /usr/bin/make -C auxprogs/joingenes make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/joingenes' g++ -c -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 joingenes.cpp g++ -c -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_transcript.cpp g++ -c -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 jg_ios.cpp In file included from /usr/include/string.h:519, from jg_transcript.h:5, from jg_ios.cpp:1: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)’ at jg_ios.cpp:251:14: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)’ at jg_ios.cpp:79:14: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘void load(std::unordered_map, Gene*>&, std::string&, int&, std::unordered_map, bool>&, Properties&)’ at jg_ios.cpp:148:9: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ specified bound 300 equals destination size [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now joingenes.o jg_transcript.o jg_ios.o -o joingenes mkdir -p ../../bin/ cp joingenes ../../bin/ make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/joingenes' dh_auto_build make -j4 "INSTALL=install --strip-program=true" make[2]: Entering directory '/<>/augustus-3.4.0+dfsg2' mkdir -p bin cd src && make make[3]: Entering directory '/<>/augustus-3.4.0+dfsg2/src' g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PP::Column&}; _Tp = PP::Column; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/11/bits/stl_vector.h: In constructor ‘PP::Block::Block(PP::DistanceType, const std::vector >&, std::string)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘bool PP::Block::_ZN2PP5Block14initThresholdsEv.part.0()’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void PP::Profile::parse_stream(std::istream&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/11/bits/stl_vector.h: In member function ‘bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map*)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:61, from ../include/types.hh:39, from ../include/geneticcode.hh:12, from ../include/pp_profile.hh:16, from pp_profile.cc:11: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PP::BonusProbEntry&}; _Tp = PP::BonusProbEntry; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/stl_tree.h: In member function ‘void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2492:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2492 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_tree.h:2492:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ /usr/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2510:19: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2510 | _M_erase_aux(__p.first, __p.second); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2161:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2161 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_tree.h: In member function ‘void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)’: /usr/include/c++/11/bits/stl_tree.h:1238:21: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 1238 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/stl_map.h: In member function ‘void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/stl_tree.h: In member function ‘virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)’: /usr/include/c++/11/bits/stl_tree.h:1238:21: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 1238 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/stl_map.h: In member function ‘virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h: In member function ‘void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/stl_tree.h: In member function ‘virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)’: /usr/include/c++/11/bits/stl_tree.h:1238:21: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 1238 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/pp_scoring.hh:16, from pp_scoring.cc:10: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from statemodel.cc:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void StateModel::initPredecessors(Matrix&, int)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from types.cc:8: /usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from types.cc:8: /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In function ‘Double quantile(const std::vector&, float)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from types.cc:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In static member function ‘static void Constant::init()’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:12, from ../include/motif.hh:13, from ../include/gene.hh:12, from gene.cc:8: /usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:12, from ../include/motif.hh:13, from ../include/gene.hh:12, from gene.cc:8: /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/motif.hh:12, from motif.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from ../include/matrix.hh:12, from ../include/motif.hh:12, from motif.cc:10: /usr/include/c++/11/bits/stl_vector.h: In member function ‘Double Motif::getProbThreshold(double, int)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/string.h:519, from /usr/include/c++/11/cstring:42, from ../include/types.hh:34, from ../include/hints.hh:12, from hints.cc:10: In function ‘char* strncpy(char*, const char*, size_t)’, inlined from ‘std::istream& operator>>(std::istream&, Feature&)’ at hints.cc:82:9: /usr/include/arm-linux-gnueabihf/bits/string_fortified.h:95:34: warning: ‘char* __builtin_strncpy(char*, const char*, unsigned int)’ output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation] 95 | return __builtin___strncpy_chk (__dest, __src, __len, | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 96 | __glibc_objsize (__dest)); | ~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/motif.hh:12, from ../include/gene.hh:12, from gene.cc:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In function ‘void examineBaseCountOfGeneSeq(AnnoSequence*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:12, from ../include/motif.hh:13, from ../include/gene.hh:12, from gene.cc:8: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/list:64, from ../include/vitmatrix.hh:17, from ../include/pp_scoring.hh:16, from ../include/gene.hh:13, from gene.cc:8: /usr/include/c++/11/bits/list.tcc: In member function ‘std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(std::__cxx11::list<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator; = void; _Tp = PP::Match; _Alloc = std::allocator]’: /usr/include/c++/11/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::__cxx11::list::const_iterator’ changed in GCC 7.1 133 | list<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::_List_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/list.tcc:133:7: note: parameter passing for argument of type ‘std::_List_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/list.tcc: In function ‘void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator; _Tp = PP::Match; _Alloc = std::allocator]’: /usr/include/c++/11/bits/list.tcc:308:7: note: parameter passing for argument of type ‘std::_List_const_iterator’ changed in GCC 7.1 308 | list<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/list.tcc:308:7: note: parameter passing for argument of type ‘std::_List_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/list.tcc:320:17: note: parameter passing for argument of type ‘std::__cxx11::list::const_iterator’ changed in GCC 7.1 320 | insert(__last1, __first2, __last2); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/list.tcc:320:17: note: parameter passing for argument of type ‘std::_List_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/list.tcc: In copy constructor ‘Gene::Gene(const Gene&)’: /usr/include/c++/11/bits/list.tcc:286:29: note: parameter passing for argument of type ‘std::_List_const_iterator’ changed in GCC 7.1 286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/list.tcc: In static member function ‘static StatePath* StatePath::condenseStatePath(StatePath*)’: /usr/include/c++/11/bits/list.tcc:286:29: note: parameter passing for argument of type ‘std::_List_const_iterator’ changed in GCC 7.1 286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type()); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/statemodel.hh:13, from ../include/intronmodel.hh:11, from intronmodel.cc:8: /usr/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from ../include/statemodel.hh:13, from ../include/intronmodel.hh:11, from intronmodel.cc:8: /usr/include/c++/11/bits/stl_map.h: In static member function ‘static Double IntronModel::dSSProb(int, bool)’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h: In static member function ‘static Double IntronModel::aSSProb(int, bool)’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/hints.hh:12, from ../include/extrinsicinfo.hh:15, from extrinsicinfo.cc:10: /usr/include/c++/11/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity; _Compare = std::less; _Alloc = std::allocator]’: /usr/include/c++/11/bits/stl_tree.h:2161:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::less, std::allocator >::const_iterator’ changed in GCC 7.1 2161 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/hints.hh:12, from ../include/extrinsicinfo.hh:15, from extrinsicinfo.cc:10: /usr/include/c++/11/bits/stl_algo.h: In function ‘_OutputIterator std::__set_difference(_InputIterator1, _InputIterator1, _InputIterator2, _InputIterator2, _OutputIterator, _Compare) [with _InputIterator1 = std::_Rb_tree_const_iterator; _InputIterator2 = std::_Rb_tree_const_iterator; _OutputIterator = std::insert_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:5356:5: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5356 | __set_difference(_InputIterator1 __first1, _InputIterator1 __last1, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:5356:5: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5356:5: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5356:5: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ /usr/include/c++/11/bits/stl_algo.h: In member function ‘void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)’: /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 5421 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1, | ^ /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5421:46: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, from vitmatrix.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ViterbiSubmapType&}; _Tp = ViterbiSubmapType; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from vitmatrix.cc:10: /usr/include/c++/11/bits/stl_tree.h: In member function ‘void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2492:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2492 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_tree.h:2492:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_tree.h: In member function ‘void ViterbiSubmapType::useMaximum(Double&)’: /usr/include/c++/11/bits/stl_tree.h:1238:21: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 1238 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_tree.h:1238:21: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 1238 | _M_erase_aux(__first, __last); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_tree.h: In member function ‘int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)’: /usr/include/c++/11/bits/stl_tree.h:2510:19: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2510 | _M_erase_aux(__p.first, __p.second); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, from vitmatrix.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void ViterbiColumnType::addState(int, signed char)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/vitmatrix.hh:12, from vitmatrix.cc:10: /usr/include/c++/11/bits/stl_vector.h: In member function ‘ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/map:60, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from vitmatrix.cc:10: /usr/include/c++/11/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2161:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2161 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = SubstateId; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:61, from ../include/types.hh:39, from ../include/vitmatrix.hh:12, from vitmatrix.cc:10: /usr/include/c++/11/bits/stl_map.h: In member function ‘void ViterbiSubmapType::registerPredecessors()’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/merkmal.hh:14, from merkmal.cc:10: /usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/merkmal.hh:14, from merkmal.cc:10: /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1799:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1799 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In static member function ‘static std::vector CRF::capOutliers(std::vector)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/merkmal.hh:14, from merkmal.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/merkmal.hh:14, from merkmal.cc:10: /usr/include/c++/11/bits/stl_algo.h: In member function ‘void BinnedMMGroup::trainBins(int)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/merkmal.hh:14, from merkmal.cc:10: /usr/include/c++/11/bits/stl_vector.h: In static member function ‘static void CRF::onlineLargeMarginTraining(Parameters*, std::vector, FeatureCollection&)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/motif.hh:12, from ../include/gene.hh:12, from ../include/mea.hh:11, from mea.cc:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In constructor ‘AugustusGraph::AugustusGraph(std::__cxx11::list*, const char*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o parser/parse.o parser/parse.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o scanner/lex.o scanner/lex.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o genomicMSA.o genomicMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o geneMSA.o geneMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/ncmodel.hh:11, from ncmodel.cc:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/ncmodel.hh:11, from ncmodel.cc:8: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void NcModel::computeLengthDistributions()’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o contTimeMC.o contTimeMC.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/motif.hh:12, from ../include/gene.hh:12, from ../include/randseqaccess.hh:12, from randseqaccess.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {hints}; _Tp = hints; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void mysqlpp::Query::storein_sequence(Sequence&, const mysqlpp::SQLTypeAdapter&) [with Sequence = std::vector]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/bits/stl_algo.h:61, from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:12, from contTimeMC.cc:10: /usr/include/c++/11/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_heap.h:223:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from ../include/types.hh:38, from ../include/geneticcode.hh:12, from contTimeMC.cc:10: /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1819 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1819:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1925 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1925:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:1939:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h: In member function ‘void Evo::setBranchLengths(std::vector, int)’: /usr/include/c++/11/bits/stl_algo.h:1954:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1954 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1955 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1956 | __comp); | ~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1866:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1866 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:1871:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1871 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, from contTimeMC.cc:9: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, from contTimeMC.cc:9: /usr/include/c++/11/bits/stl_vector.h: In member function ‘virtual void ExonEvo::addBranchLength(double)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonevo.o codonevo.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o compgenepred.o compgenepred.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, from ../include/codonevo.hh:11, from codonevo.cc:9: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, from ../include/codonevo.hh:11, from codonevo.cc:9: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void CodonEvo::setPrior(double)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, from ../include/codonevo.hh:11, from codonevo.cc:9: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void CodonEvo::setOmegas(int)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘double CodonEvo::estOmegaOnSeqTuple(std::vector >&, PhyloTree*, int&)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/matrix.hh:12, from ../include/contTimeMC.hh:13, from ../include/codonevo.hh:11, from codonevo.cc:9: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void CodonEvo::setAAPostProbs()’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from geneMSA.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o phylotree.o phylotree.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/geneticcode.hh:12, from geneMSA.cc:10: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void GeneMSA::calcConsScore(std::__cxx11::list&, const std::vector&, std::string)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthograph.o orthograph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/hints.hh:12, from ../include/extrinsicinfo.hh:15, from ../include/compgenepred.hh:12, from compgenepred.cc:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/phylotree.hh:13, from phylotree.cc:12: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/phylotree.hh:13, from phylotree.cc:12: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void Treenode::resizeTable(int, double)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘double PhyloTree::pruningAlgor(std::vector&, Evo*, int)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In constructor ‘AugustusGraph::AugustusGraph(std::__cxx11::list*, const char*)’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘int PhyloTree::fitch(std::vector&, int)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘double PhyloTree::MAP(std::vector&, std::vector&, Evo*, bool)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/phylotree.hh:13, from phylotree.cc:12: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/vector.tcc: In member function ‘void PhyloTree::getBranchLengths(std::vector&) const’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘void GeneMSA::computeOmegasEff(std::__cxx11::list&, const std::vector&, PhyloTree*, std::ofstream*)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void CompGenePred::runPredictionOrTest()’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/hints.hh:12, from ../include/extrinsicinfo.hh:15, from ../include/compgenepred.hh:12, from compgenepred.cc:8: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o orthoexon.o orthoexon.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o alignment.o alignment.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/exoncand.hh:13, from ../include/orthoexon.hh:11, from orthoexon.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 509 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/types.hh:36, from ../include/exoncand.hh:13, from ../include/orthoexon.hh:11, from orthoexon.cc:10: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void OrthoExon::setOmega(std::vector*, CodonEvo*, bool)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In constructor ‘OrthoExon::OrthoExon(int_fast64_t, size_t)’: /usr/include/c++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 960 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o speciesgraph.o speciesgraph.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o codonMSA.o codonMSA.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o train_logReg_param.o train_logReg_param.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o tokenizer.o tokenizer.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o sqliteDB.o sqliteDB.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/intronmodel.hh:11, from introntrain.cc:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/exonmodel.hh:11, from exontrain.cc:8: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/intronmodel.hh:11, from introntrain.cc:8: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void IntronModel::makeDSSProbs()’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h: In member function ‘void IntronModel::buildProbabilities(const AnnoSequence*)’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:67, from ../include/matrix.hh:12, from ../include/statemodel.hh:12, from ../include/exonmodel.hh:11, from exontrain.cc:8: /usr/include/c++/11/bits/stl_vector.h: In member function ‘void ExonModel::buildProbabilities()’: /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1198 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp prepareAlign ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from ../include/properties.hh:14, from ../include/pp_simscore.hh:21, from pp_simscore.cc:10: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ cp load2sqlitedb ../bin/ echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE" > cxxflags g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 /usr/include/c++/11/bits/vector.tcc: In member function ‘void SS::SimilarityScore::printAlignment()’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cp pp_simScore ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 cp getSeq ../bin/ cp load2db ../bin/ g++ -Wdate-time -D_FORTIFY_SOURCE=2 -DZIPINPUT -DCOMPGENEPRED -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -I/usr/include/lpsolve -I/usr/include/mysql -I/usr/include/mysql++ -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lmysqlclient -lmysqlpp -lsqlite3 In file included from /usr/include/c++/11/vector:72, from ../include/types.hh:36, from etraining.cc:9: /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In static member function ‘static void CRF::compareWeights(Parameters*, std::vector&, std::vector&, int) [with U = double; V = double]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cp fastBlockSearch ../bin/ cp etraining ../bin/ cp augustus ../bin/ make[3]: Leaving directory '/<>/augustus-3.4.0+dfsg2/src' cd auxprogs && make make[3]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs' cd aln2wig; make; make[4]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/aln2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'aln2wig' is up to date. make[4]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/aln2wig' cd bam2hints; make; make[4]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2hints' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'bam2hints' is up to date. make[4]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2hints' cd compileSpliceCands; make; make[4]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'compileSpliceCands' is up to date. make[4]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/compileSpliceCands' cd filterBam; make; make[4]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src;make) make[5]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' g++ -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -ffile-prefix-map=/<>/augustus-3.4.0+dfsg2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz filterBam compiled with BAMTOOLS=/usr/include/bamtools mkdir -p ../../../bin mv filterBam ../../../bin/filterBam make[5]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam/src' make[4]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/filterBam' cd homGeneMapping; make; make[4]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. (cd src; make) make[5]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' make[5]: Nothing to be done for 'all'. make[5]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping/src' make[4]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/homGeneMapping' cd joingenes; make; make[4]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/joingenes' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: Nothing to be done for 'all'. make[4]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/joingenes' cd utrrnaseq/Debug; make all; make[4]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. Building file: ../src/Compute_UTRs.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp" In file included from /usr/include/c++/11/map:61, from ../src/Compute_UTRs.hpp:14, from ../src/Compute_UTRs.cpp:8: /usr/include/c++/11/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 502 | std::tuple(__k), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 503 | std::tuple<>()); | ~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](std::map<_Key, _Tp, _Compare, _Alloc>::key_type&&) [with _Key = unsigned int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_map.h:520:44: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 520 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 521 | std::forward_as_tuple(std::move(__k)), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 522 | std::tuple<>()); | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/map:60, from ../src/Compute_UTRs.hpp:14, from ../src/Compute_UTRs.cpp:8: /usr/include/c++/11/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2426 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/11/bits/stl_tree.h:2161:5: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ changed in GCC 7.1 2161 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Finished building: ../src/Compute_UTRs.cpp Building file: ../src/Coord_Transform.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp" Finished building: ../src/Coord_Transform.cpp Building file: ../src/Genomic_Data.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp" Finished building: ../src/Genomic_Data.cpp Building file: ../src/Splice_Sites.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp" Finished building: ../src/Splice_Sites.cpp Building file: ../src/Supporting_Methods.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp" Finished building: ../src/Supporting_Methods.cpp Building file: ../src/Test.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp" Finished building: ../src/Test.cpp Building file: ../src/UTRs.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp" ../src/UTRs.cpp: In static member function ‘static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map&)’: ../src/UTRs.cpp:387:66: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 387 | vector::iterator jt = min_element(d.begin(), d.end()); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/algorithm:62, from ../src/UTRs.cpp:20: /usr/include/c++/11/bits/stl_algo.h: In function ‘constexpr _FIter std::min_element(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator > >]’: /usr/include/c++/11/bits/stl_algo.h:5639:12: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 5639 | inline min_element(_ForwardIterator __first, _ForwardIterator __last) | ^~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:5639:12: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5648:43: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 5648 | return _GLIBCXX_STD_A::__min_element(__first, __last, | ^ In file included from /usr/include/c++/11/bits/stl_algobase.h:71, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from ../src/Genomic_Data.hpp:8, from ../src/UTRs.cpp:5: /usr/include/c++/11/bits/predefined_ops.h: In member function ‘constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = __gnu_cxx::__normal_iterator > >; _Iterator2 = __gnu_cxx::__normal_iterator > >]’: /usr/include/c++/11/bits/predefined_ops.h:44:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 44 | operator()(_Iterator1 __it1, _Iterator2 __it2) const | ^~~~~~~~ /usr/include/c++/11/bits/predefined_ops.h:44:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 In file included from /usr/include/c++/11/algorithm:62, from ../src/UTRs.cpp:20: /usr/include/c++/11/bits/stl_algo.h: In function ‘constexpr _ForwardIterator std::__min_element(_ForwardIterator, _ForwardIterator, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/11/bits/stl_algo.h:5617:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 5617 | __min_element(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~~~ /usr/include/c++/11/bits/stl_algo.h:5617:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 /usr/include/c++/11/bits/stl_algo.h:5624:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 5624 | if (__comp(__first, __result)) | ~~~~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/11/vector:72, from ../src/Genomic_Data.hpp:9, from ../src/UTRs.cpp:5: /usr/include/c++/11/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ Finished building: ../src/UTRs.cpp Building file: ../src/main.cpp Invoking: GCC C++ Compiler g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp" Finished building: ../src/main.cpp Building target: utrrnaseq Invoking: GCC C++ Linker g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o Finished building target: utrrnaseq make[4]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/utrrnaseq/Debug' cd bam2wig; make; make[4]: Entering directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2wig' make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[4]: 'bam2wig' is up to date. make[4]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs/bam2wig' make[3]: Leaving directory '/<>/augustus-3.4.0+dfsg2/auxprogs' make[2]: Leaving directory '/<>/augustus-3.4.0+dfsg2' asciidoctor -a docdate='' -b manpage --destination-dir=debian/mansrc/ mansrc/*adoc make[1]: Leaving directory '/<>/augustus-3.4.0+dfsg2' dh_auto_test -a make -j4 test make[1]: Entering directory '/<>/augustus-3.4.0+dfsg2' cd tests/examples && ./testcases.py --html test_utr_on (__main__.TestAugustus) ... ok test_hints_MPE (__main__.TestAugustus) ... ok test_training_new_species (__main__.TestAugustus) ... ok test_ab_initio_prediction (__main__.TestAugustus) ... ok test_format_and_error_out (__main__.TestAugustus) ... ok test_cgp (__main__.TestAugustus) ... ok test_cgp_sqlite (__main__.TestAugustus) ... ok test_cgp_sqlite_hints (__main__.TestAugustus) ... ok ---------------------------------------------------------------------- Ran 8 tests in 1435.157s OK Removing generated test files... ---------------------------------------------------------------------- Executing small test suite ---------------------------------------------------------------------- Creating SQLite database for cgp test cases... tests/auxprogs/bam2wig/test_bam2wig.py --html test_bam2wig (__main__.TestBam2Wig) ... ok test_bam2wig_region (__main__.TestBam2Wig) ... ok ---------------------------------------------------------------------- Ran 2 tests in 0.038s OK make[1]: Leaving directory '/<>/augustus-3.4.0+dfsg2' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>/augustus-3.4.0+dfsg2' mkdir -p debian/augustus/usr/bin install bin/* debian/augustus/usr/bin install auxprogs/bam2wig/bam2wig \ debian/augustus/usr/bin install auxprogs/compileSpliceCands/compileSpliceCands \ debian/augustus/usr/bin install auxprogs/homGeneMapping/src/homGeneMapping \ debian/augustus/usr/bin install auxprogs/joingenes/joingenes \ debian/augustus/usr/bin mkdir -p debian/augustus/usr/share/augustus cp -r scripts debian/augustus/usr/share/augustus chmod -R -x debian/augustus/usr/share/augustus/scripts/* rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \ debian/augustus/usr/share/augustus/scripts/executeTestCGP.py \ debian/augustus/usr/share/augustus/scripts/*.txt chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \ debian/augustus/usr/share/augustus/scripts/*.pl* mkdir -p debian/augustus-doc/usr/share/doc/augustus cp README* debian/augustus-doc/usr/share/doc/augustus cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus cp docs/RUNNING* debian/augustus-doc/usr/share/doc/augustus cp docs/README* debian/augustus-doc/usr/share/doc/augustus cp docs/EXONCAND-MSAS-CGP.md \ debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial \ debian/augustus-doc/usr/share/doc/augustus cp -r docs/tutorial-cgp \ debian/augustus-doc/usr/share/doc/augustus mkdir -p debian/augustus-data/usr/share/augustus cp -r config debian/augustus-data/usr/share/augustus find debian/augustus-data/usr/share/augustus \ -type f -exec chmod -x {} \; make[1]: Leaving directory '/<>/augustus-3.4.0+dfsg2' dh_installdocs -a debian/rules override_dh_installchangelogs make[1]: Entering directory '/<>/augustus-3.4.0+dfsg2' dh_installchangelogs -k docs/HISTORY.TXT make[1]: Leaving directory '/<>/augustus-3.4.0+dfsg2' dh_installman -a dh_perl -a dh_link -a dh_strip_nondeterminism -a debian/rules override_dh_compress make[1]: Entering directory '/<>/augustus-3.4.0+dfsg2' dh_compress -Xtutorial make[1]: Leaving directory '/<>/augustus-3.4.0+dfsg2' dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a debugedit: debian/augustus/usr/bin/aln2wig: Unknown DWARF DW_FORM_0x1f21 ab5b797c8533e36cf34f12984dbc2ae49429b93e debugedit: debian/augustus/usr/bin/load2sqlitedb: Unknown DWARF DW_FORM_0x1f21 f2d7d7dfb83194a438c9d7fc32c1c545b878cfa0 debugedit: debian/augustus/usr/bin/getSeq: Unknown DWARF DW_FORM_0x1f21 9bd20c4e31a85935c86e3a97b63faa84c599eb8d debugedit: debian/augustus/usr/bin/augustus: Unknown DWARF DW_FORM_0x1f21 8594b6957f3eb00ddc9d83437709f05994ecae35 debugedit: debian/augustus/usr/bin/prepareAlign: Unknown DWARF DW_FORM_0x1f21 0c641a7ec34bc882ed5258fd8b2dd66eb9ff8515 debugedit: debian/augustus/usr/bin/load2db: Unknown DWARF DW_FORM_0x1f21 482dd201076df19bcc1bd40ef7a376e2ddc423ce debugedit: debian/augustus/usr/bin/joingenes: Unknown DWARF DW_FORM_0x1f21 50d5d60c7e60def9ea973199f5e2f4e262e5111a debugedit: debian/augustus/usr/bin/compileSpliceCands: Unknown DWARF DW_FORM_0x1f20 d9f951b00505b8efeb31e315c651ec73b4b8dfa1 debugedit: debian/augustus/usr/bin/homGeneMapping: Unknown DWARF DW_FORM_0x1f21 be4ea013110e4e0f701685b0676c21bd185a1161 debugedit: debian/augustus/usr/bin/bam2hints: Unknown DWARF DW_FORM_0x1f21 cba20c2527855bdd6f88cc7e5236a5a326b0b33d debugedit: debian/augustus/usr/bin/pp_simScore: Unknown DWARF DW_FORM_0x1f21 ab816ac7dcfb0839a65078797b3ccb2f3426bb7a debugedit: debian/augustus/usr/bin/bam2wig: Unknown DWARF DW_FORM_0x1f21 ce8e0b938c55f3ecaca3218568fb2230c1c5fbeb debugedit: debian/augustus/usr/bin/filterBam: Unknown DWARF DW_FORM_0x1f21 77363f47cd3467d6f80c7ab298b8c44d5900ea75 debugedit: debian/augustus/usr/bin/etraining: Unknown DWARF DW_FORM_0x1f21 d829e806dd8c4d96b1fbec779dbab4699075ac7e debugedit: debian/augustus/usr/bin/fastBlockSearch: Unknown DWARF DW_FORM_0x1f20 ba76928c547b05dfb0ed74c2de262b94b3f212fb dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/augustus/usr/bin/getSeq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/filterBam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/pp_simScore contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/homGeneMapping contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2db contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/prepareAlign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/load2sqlitedb contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/fastBlockSearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/augustus/usr/bin/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a INFO: pkgstriptranslations version 149 INFO: pkgstriptranslations version 149 pkgstriptranslations: processing augustus (in debian/augustus); do_strip: , oemstrip: pkgstriptranslations: processing augustus-dbgsym (in debian/.debhelper/augustus/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgmaintainermangler: Not overriding Maintainer for domain lists.ubuntu.com pkgstripfiles: processing control file: debian/augustus/DEBIAN/control, package augustus, directory debian/augustus pkgstripfiles: processing control file: debian/.debhelper/augustus/dbgsym-root/DEBIAN/control, package augustus-dbgsym, directory debian/.debhelper/augustus/dbgsym-root dpkg-deb: building package 'augustus-dbgsym' in 'debian/.debhelper/scratch-space/build-augustus/augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.deb'. .. removing usr/share/doc/augustus/changelog.gz pkgstripfiles: Truncating usr/share/doc/augustus/changelog.Debian.gz to topmost ten records pkgstripfiles: Running PNG optimization (using 4 cpus) for package augustus ... pkgstripfiles: No PNG files. dpkg-deb: building package 'augustus' in '../augustus_3.4.0+dfsg2-3build1_armhf.deb'. Renaming augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.deb to augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../augustus_3.4.0+dfsg2-3build1_armhf.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 2021-12-07T18:11:03Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ augustus_3.4.0+dfsg2-3build1_armhf.changes: ------------------------------------------- Format: 1.8 Date: Tue, 07 Dec 2021 17:24:14 +0000 Source: augustus Binary: augustus Built-For-Profiles: noudeb Architecture: armhf Version: 3.4.0+dfsg2-3build1 Distribution: jammy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Steve Langasek Description: augustus - gene prediction in eukaryotic genomes Changes: augustus (3.4.0+dfsg2-3build1) jammy; urgency=medium . * No-change rebuild against libgsl27 Checksums-Sha1: 3dc8ed5506e6b51f70adbc9936c2c256d5075e5e 34850756 augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.ddeb ac3988c3934b18c116450ec7a340d701aba76fe9 9386 augustus_3.4.0+dfsg2-3build1_armhf.buildinfo 3f73d8f6ae9e0ffbccb27333b76dbf767141c803 1840008 augustus_3.4.0+dfsg2-3build1_armhf.deb Checksums-Sha256: 30ea79af96d105610cb0de8cde72d961aa02e0cc63249dcb7b2f5b98a37ab851 34850756 augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.ddeb 9d89321a017b30ab1edf651c085d48463eae6a157218ea51335e025d41b1bc73 9386 augustus_3.4.0+dfsg2-3build1_armhf.buildinfo 891db3be081eab4e0177ca3aa7cb28e76119600ba350da877dfddc69a8da6b0e 1840008 augustus_3.4.0+dfsg2-3build1_armhf.deb Files: 55e178fe3003e384412a049fa2d0d043 34850756 debug optional augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.ddeb d6d280bf5b310092a13b409aeecf1ee0 9386 science optional augustus_3.4.0+dfsg2-3build1_armhf.buildinfo e90d3d60f2630007490310891b48a021 1840008 science optional augustus_3.4.0+dfsg2-3build1_armhf.deb Original-Maintainer: Debian Med Packaging Team +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: augustus Binary: augustus augustus-dbgsym Architecture: armhf Version: 3.4.0+dfsg2-3build1 Checksums-Md5: 55e178fe3003e384412a049fa2d0d043 34850756 augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.ddeb e90d3d60f2630007490310891b48a021 1840008 augustus_3.4.0+dfsg2-3build1_armhf.deb Checksums-Sha1: 3dc8ed5506e6b51f70adbc9936c2c256d5075e5e 34850756 augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.ddeb 3f73d8f6ae9e0ffbccb27333b76dbf767141c803 1840008 augustus_3.4.0+dfsg2-3build1_armhf.deb Checksums-Sha256: 30ea79af96d105610cb0de8cde72d961aa02e0cc63249dcb7b2f5b98a37ab851 34850756 augustus-dbgsym_3.4.0+dfsg2-3build1_armhf.ddeb 891db3be081eab4e0177ca3aa7cb28e76119600ba350da877dfddc69a8da6b0e 1840008 augustus_3.4.0+dfsg2-3build1_armhf.deb Build-Origin: Ubuntu Build-Architecture: armhf Build-Date: Tue, 07 Dec 2021 18:11:01 +0000 Build-Path: /<>/augustus-3.4.0+dfsg2 Build-Tainted-By: merged-usr-via-aliased-dirs usr-local-has-programs Installed-Build-Depends: asciidoctor (= 2.0.16-2), autoconf (= 2.71-2), automake (= 1:1.16.5-1.1), autopoint (= 0.21-4ubuntu3), autotools-dev (= 20180224.1+nmu1), base-files (= 12ubuntu2), base-passwd (= 3.5.52), bash (= 5.1-5ubuntu1), binutils (= 2.37-10ubuntu1), binutils-arm-linux-gnueabihf (= 2.37-10ubuntu1), binutils-common (= 2.37-10ubuntu1), bsdextrautils (= 2.37.2-4ubuntu1), bsdutils (= 1:2.37.2-4ubuntu1), build-essential (= 12.9ubuntu2), bzip2 (= 1.0.8-5), ca-certificates (= 20211016), coreutils (= 8.32-4ubuntu3), cpp (= 4:11.2.0-1ubuntu1), cpp-11 (= 11.2.0-12ubuntu1), dash (= 0.5.11+git20210903+057cd650a4ed-3), debconf (= 1.5.79), debhelper (= 13.5.2ubuntu1), debianutils (= 5.5-1ubuntu1), debugedit (= 1:5.0-3), default-libmysqlclient-dev (= 1.0.7), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.12.1-1), diffutils (= 1:3.8-0ubuntu1), dpkg (= 1.20.9ubuntu3), dpkg-dev (= 1.20.9ubuntu3), dwz (= 0.14-1build1), file (= 1:5.41-2), findutils (= 4.8.0-1ubuntu2), g++ (= 4:11.2.0-1ubuntu1), g++-11 (= 11.2.0-12ubuntu1), gcc (= 4:11.2.0-1ubuntu1), gcc-11 (= 11.2.0-12ubuntu1), gcc-11-base (= 11.2.0-12ubuntu1), gettext (= 0.21-4ubuntu3), gettext-base (= 0.21-4ubuntu3), grep (= 3.7-1), groff-base (= 1.22.4-7), gzip (= 1.10-4ubuntu2), hostname (= 3.23ubuntu1), icu-devtools (= 67.1-7ubuntu1), init-system-helpers (= 1.60build1), intltool-debian (= 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0.21.0-1.2build1), libpython3-stdlib (= 3.9.7-4), libpython3.9-minimal (= 3.9.9-1build1), libpython3.9-stdlib (= 3.9.9-1build1), librbio2 (= 1:5.10.1+dfsg-3), libreadline8 (= 8.1-2build1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2build3), libruby3.0 (= 3.0.2-5ubuntu1), libsasl2-2 (= 2.1.27+dfsg2-2build1), libsasl2-modules-db (= 2.1.27+dfsg2-2build1), libseccomp2 (= 2.5.2-2ubuntu2), libselinux1 (= 3.3-1build1), libsigsegv2 (= 2.13-1ubuntu2), libsliplu1 (= 1:5.10.1+dfsg-3), libsmartcols1 (= 2.37.2-4ubuntu1), libspqr2 (= 1:5.10.1+dfsg-3), libsqlite3-0 (= 3.36.0-2), libsqlite3-dev (= 3.36.0-2), libssh-4 (= 0.9.6-1build1), libssl-dev (= 3.0.0-1ubuntu1), libssl1.1 (= 1.1.1l-1ubuntu1), libssl3 (= 3.0.0-1ubuntu1), libstdc++-11-dev (= 11.2.0-12ubuntu1), libstdc++6 (= 11.2.0-12ubuntu1), libsub-override-perl (= 0.09-2), libsuitesparse-dev (= 1:5.10.1+dfsg-3), libsuitesparseconfig5 (= 1:5.10.1+dfsg-3), libsystemd0 (= 249.5-2ubuntu1), libtasn1-6 (= 4.18.0-4), libtinfo6 (= 6.3-1), libtirpc-common (= 1.3.2-2), libtirpc-dev (= 1.3.2-2), libtirpc3 (= 1.3.2-2), libtool (= 2.4.6-15build1), libubsan1 (= 11.2.0-12ubuntu1), libuchardet0 (= 0.0.7-1build1), libudev1 (= 249.5-2ubuntu1), libumfpack5 (= 1:5.10.1+dfsg-3), libunistring2 (= 0.9.10-6), libuuid1 (= 2.37.2-4ubuntu1), libxml2 (= 2.9.12+dfsg-5), libyaml-0-2 (= 0.2.2-1build1), libzstd-dev (= 1.4.8+dfsg-3), libzstd1 (= 1.4.8+dfsg-3), linux-libc-dev (= 5.15.0-13.13), login (= 1:4.8.1-2ubuntu1), lsb-base (= 11.1.0ubuntu3), lto-disabled-list (= 17), lzma-dev (= 9.22-2.2), m4 (= 1.4.18-5ubuntu1), make (= 4.3-4ubuntu2), man-db (= 2.9.4-2build1), mawk (= 1.3.4.20200120-2build1), media-types (= 4.0.0), mysql-common (= 5.8+1.0.7), ncurses-base (= 6.3-1), ncurses-bin (= 6.3-1), openssl (= 3.0.0-1ubuntu1), patch (= 2.7.6-7build1), perl (= 5.32.1-3ubuntu3), perl-base (= 5.32.1-3ubuntu3), perl-modules-5.32 (= 5.32.1-3ubuntu3), po-debconf (= 1.0.21+nmu1), python3 (= 3.9.7-4), python3-minimal (= 3.9.7-4), python3.9 (= 3.9.9-1build1), python3.9-minimal (= 3.9.9-1build1), rake (= 13.0.3-1), readline-common (= 8.1-2build1), rpcsvc-proto (= 1.4.2-0ubuntu5), ruby (= 1:3.0~exp1), ruby-asciidoctor (= 2.0.16-2), ruby-minitest (= 5.13.0-1), ruby-net-telnet (= 0.1.1-2), ruby-power-assert (= 1.1.7-2), ruby-rubygems (= 3.2.27-3), ruby-test-unit (= 3.3.9-1), ruby-xmlrpc (= 0.3.2-1), ruby3.0 (= 3.0.2-5ubuntu1), rubygems-integration (= 1.18), samtools (= 1.13-4), sed (= 4.7-1ubuntu2), sensible-utils (= 0.0.17), sysvinit-utils (= 2.96-7ubuntu2), tar (= 1.34+dfsg-1build2), tzdata (= 2021e-1ubuntu1), util-linux (= 2.37.2-4ubuntu1), xz-utils (= 5.2.5-2build1), zlib1g (= 1:1.2.11.dfsg-2ubuntu7), zlib1g-dev (= 1:1.2.11.dfsg-2ubuntu7) Environment: DEB_BUILD_OPTIONS="parallel=4" DEB_BUILD_PROFILES="noudeb" LANG="C.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1638897854" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ augustus_3.4.0+dfsg2-3build1_armhf.deb -------------------------------------- new Debian package, version 2.0. size 1840008 bytes: control archive=5004 bytes. 1616 bytes, 24 lines control 10236 bytes, 137 lines md5sums Package: augustus Version: 3.4.0+dfsg2-3build1 Architecture: armhf Maintainer: Ubuntu Developers Installed-Size: 6797 Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libboost-iostreams1.74.0 (>= 1.74.0), libc6 (>= 2.34), libcolamd2 (>= 1:4.5.2), libgcc-s1 (>= 3.5), libgsl27 (>= 2.7.1), libhts3 (>= 1.10), libmysql++3v5 (>= 3.2.5-1~), libmysqlclient21 (>= 8.0.11), libsqlite3-0 (>= 3.5.9), libstdc++6 (>= 11), augustus-data Recommends: samtools Suggests: cdbfasta, diamond-aligner, libfile-which-perl, libparallel-forkmanager-perl, libyaml-perl, libdbd-mysql-perl, python3-biopython Section: science Priority: optional Homepage: https://bioinf.uni-greifswald.de/augustus/ Description: gene prediction in eukaryotic genomes AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model (HMM), a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes. Original-Maintainer: Debian Med Packaging Team drwxr-xr-x root/root 0 2021-12-07 17:24 ./ drwxr-xr-x root/root 0 2021-12-07 17:24 ./usr/ drwxr-xr-x root/root 0 2021-12-07 17:24 ./usr/bin/ -rwxr-xr-x root/root 9772 2021-12-07 17:24 ./usr/bin/aln2wig -rwxr-xr-x root/root 1612608 2021-12-07 17:24 ./usr/bin/augustus -rwxr-xr-x root/root 26624 2021-12-07 17:24 ./usr/bin/bam2hints -rwxr-xr-x root/root 9772 2021-12-07 17:24 ./usr/bin/bam2wig -rwxr-xr-x root/root 13868 2021-12-07 17:24 ./usr/bin/compileSpliceCands -rwxr-xr-x root/root 1731392 2021-12-07 17:24 ./usr/bin/etraining -rwxr-xr-x root/root 184328 2021-12-07 17:24 ./usr/bin/fastBlockSearch -rwxr-xr-x root/root 120496 2021-12-07 17:24 ./usr/bin/filterBam -rwxr-xr-x root/root 1596368 2021-12-07 17:24 ./usr/bin/getSeq -rwxr-xr-x root/root 100212 2021-12-07 17:24 ./usr/bin/homGeneMapping -rwxr-xr-x root/root 104084 2021-12-07 17:24 ./usr/bin/joingenes -rwxr-xr-x root/root 147240 2021-12-07 17:24 ./usr/bin/load2db -rwxr-xr-x root/root 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+------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build Type: any Build-Space: n/a Build-Time: 1925 Distribution: jammy-proposed Host Architecture: armhf Install-Time: 55 Job: augustus_3.4.0+dfsg2-3build1.dsc Machine Architecture: arm64 Package: augustus Package-Time: 2006 Source-Version: 3.4.0+dfsg2-3build1 Space: n/a Status: successful Version: 3.4.0+dfsg2-3build1 -------------------------------------------------------------------------------- Finished at 2021-12-07T18:11:03Z Build needed 00:33:26, no disk space Adding user buildd to group lxd RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=jammy --arch=armhf PACKAGEBUILD-22599315 Scanning for processes to kill in build PACKAGEBUILD-22599315