https://launchpad.net/ubuntu/+source/freebayes/1.3.2-3/+build/19389663 RUN: /usr/share/launchpad-buildd/bin/builder-prep Kernel version: Linux bos02-arm64-070 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 aarch64 Buildd toolchain package versions: launchpad-buildd_188 python-lpbuildd_188 sbuild_0.67.0-2ubuntu7.1 bzr-builder_0.7.3+bzr174~ppa13~ubuntu14.10.1 bzr_2.7.0-2ubuntu3.1 git-build-recipe_0.3.6~git201906051340.ff11471~ubuntu16.04.1 git_1:2.7.4-0ubuntu1.7 dpkg-dev_1.18.4ubuntu1.6 python-debian_0.1.27ubuntu2. Syncing the system clock with the buildd NTP service... 1 Jun 11:13:10 ntpdate[1926]: adjust time server 10.211.37.1 offset 0.001954 sec RUN: /usr/share/launchpad-buildd/bin/in-target unpack-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19389663 --image-type chroot /home/buildd/filecache-default/a77e1afdcf3761e08e999e63510e3d2f5c5a8a8d Creating target for build PACKAGEBUILD-19389663 RUN: /usr/share/launchpad-buildd/bin/in-target mount-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19389663 Starting target for build PACKAGEBUILD-19389663 RUN: /usr/share/launchpad-buildd/bin/in-target override-sources-list --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19389663 'deb http://ftpmaster.internal/ubuntu groovy main universe' 'deb http://ftpmaster.internal/ubuntu groovy-security main universe' 'deb http://ftpmaster.internal/ubuntu groovy-updates main universe' 'deb http://ftpmaster.internal/ubuntu groovy-proposed main universe' Overriding sources.list in build-PACKAGEBUILD-19389663 RUN: /usr/share/launchpad-buildd/bin/in-target update-debian-chroot --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19389663 Updating target for build PACKAGEBUILD-19389663 Get:1 http://ftpmaster.internal/ubuntu groovy InRelease [268 kB] Get:2 http://ftpmaster.internal/ubuntu groovy-security InRelease [89.1 kB] Get:3 http://ftpmaster.internal/ubuntu groovy-updates InRelease [89.1 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed InRelease [119 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf Packages [935 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main Translation-en [507 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/universe armhf Packages [8425 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/universe Translation-en [5180 kB] Get:9 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf Packages [43.3 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main Translation-en [25.6 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf Packages [437 kB] Get:12 http://ftpmaster.internal/ubuntu groovy-proposed/universe Translation-en [285 kB] Fetched 16.4 MB in 6s (2764 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-files binutils binutils-arm-linux-gnueabihf binutils-common bsdutils bzip2 cpp-9 dash debconf debianutils e2fsprogs fdisk g++-9 gcc-10-base gcc-9 gcc-9-base gpg gpg-agent gpgconf gpgv gzip libacl1 libapparmor1 libapt-pkg6.0 libasan5 libatomic1 libbinutils libblkid1 libbz2-1.0 libcap2 libcc1-0 libcom-err2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libdevmapper1.02.1 libext2fs2 libfdisk1 libgcc-9-dev libgcc-s1 libgomp1 libidn2-0 libkmod2 libmount1 libncurses6 libncursesw6 libperl5.30 libprocps8 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libstdc++-9-dev libstdc++6 libsystemd0 libtinfo6 libubsan1 libudev1 libuuid1 linux-libc-dev login logsave make mount ncurses-base ncurses-bin passwd perl perl-base perl-modules-5.30 procps systemd systemd-sysv systemd-timesyncd sysvinit-utils tzdata util-linux 80 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 47.4 MB of archives. After this operation, 434 kB of additional disk space will be used. Get:1 http://ftpmaster.internal/ubuntu groovy/main armhf libcrypt-dev armhf 1:4.4.15-1ubuntu1 [120 kB] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf libcrypt1 armhf 1:4.4.15-1ubuntu1 [93.4 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf base-files armhf 11ubuntu7 [59.7 kB] Get:4 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf bsdutils armhf 1:2.35.1-5ubuntu2 [78.9 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf debianutils armhf 4.11 [84.3 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf perl-modules-5.30 all 5.30.2-1 [2740 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf libperl5.30 armhf 5.30.2-1 [3296 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf perl armhf 5.30.2-1 [224 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf perl-base armhf 5.30.2-1 [1409 kB] Get:10 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf bzip2 armhf 1.0.8-3 [31.8 kB] Get:11 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libbz2-1.0 armhf 1.0.8-3 [31.0 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf debconf all 1.5.74 [121 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf dash armhf 0.5.10.2-7 [79.2 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf gzip armhf 1.10-2ubuntu1 [90.8 kB] Get:15 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf login armhf 1:4.8.1-1ubuntu6 [217 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main armhf ncurses-bin armhf 6.2-1 [164 kB] Get:17 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libblkid1 armhf 2.35.1-5ubuntu2 [120 kB] Get:18 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libuuid1 armhf 2.35.1-5ubuntu2 [21.5 kB] Get:19 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libfdisk1 armhf 2.35.1-5ubuntu2 [159 kB] Get:20 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libmount1 armhf 2.35.1-5ubuntu2 [132 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main armhf libncurses6 armhf 6.2-1 [79.7 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main armhf libncursesw6 armhf 6.2-1 [106 kB] Get:23 http://ftpmaster.internal/ubuntu groovy/main armhf libtinfo6 armhf 6.2-1 [73.6 kB] Get:24 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsmartcols1 armhf 2.35.1-5ubuntu2 [84.3 kB] Get:25 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf fdisk armhf 2.35.1-5ubuntu2 [113 kB] Get:26 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf util-linux armhf 2.35.1-5ubuntu2 [985 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf ncurses-base all 6.2-1 [18.7 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf sysvinit-utils armhf 2.96-3ubuntu1 [19.1 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main armhf libatomic1 armhf 10.1.0-3ubuntu1 [7184 B] Get:30 http://ftpmaster.internal/ubuntu groovy/main armhf libubsan1 armhf 10.1.0-3ubuntu1 [121 kB] Get:31 http://ftpmaster.internal/ubuntu groovy/main armhf libgomp1 armhf 10.1.0-3ubuntu1 [86.9 kB] Get:32 http://ftpmaster.internal/ubuntu groovy/main armhf gcc-10-base armhf 10.1.0-3ubuntu1 [20.0 kB] Get:33 http://ftpmaster.internal/ubuntu groovy/main armhf libgcc-s1 armhf 10.1.0-3ubuntu1 [36.2 kB] Get:34 http://ftpmaster.internal/ubuntu groovy/main armhf libcc1-0 armhf 10.1.0-3ubuntu1 [34.6 kB] Get:35 http://ftpmaster.internal/ubuntu groovy/main armhf libstdc++6 armhf 10.1.0-3ubuntu1 [440 kB] Get:36 http://ftpmaster.internal/ubuntu groovy/main armhf systemd-sysv armhf 245.5-3ubuntu1 [10.3 kB] Get:37 http://ftpmaster.internal/ubuntu groovy/main armhf systemd-timesyncd armhf 245.5-3ubuntu1 [27.9 kB] Get:38 http://ftpmaster.internal/ubuntu groovy/main armhf libacl1 armhf 2.2.53-8 [16.0 kB] Get:39 http://ftpmaster.internal/ubuntu groovy/main armhf libapparmor1 armhf 2.13.3-7ubuntu6 [29.2 kB] Get:40 http://ftpmaster.internal/ubuntu groovy/main armhf libcap2 armhf 1:2.34-2 [15.6 kB] Get:41 http://ftpmaster.internal/ubuntu groovy/main armhf libudev1 armhf 245.5-3ubuntu1 [67.1 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main armhf libdevmapper1.02.1 armhf 2:1.02.167-1ubuntu3 [118 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main armhf libcryptsetup12 armhf 2:2.3.1-1ubuntu1 [172 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main armhf libidn2-0 armhf 2.3.0-1 [49.9 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main armhf libkmod2 armhf 27+20200310-2ubuntu1 [38.2 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main armhf libseccomp2 armhf 2.4.3-1ubuntu2 [32.4 kB] Get:47 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf mount armhf 2.35.1-5ubuntu2 [112 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main armhf systemd armhf 245.5-3ubuntu1 [3644 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main armhf libsystemd0 armhf 245.5-3ubuntu1 [245 kB] Get:50 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libapt-pkg6.0 armhf 2.1.5 [757 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main armhf gpgv armhf 2.2.20-1ubuntu1 [170 kB] Get:52 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf apt armhf 2.1.5 [1244 kB] Get:53 http://ftpmaster.internal/ubuntu groovy/main armhf logsave armhf 1.45.6-1ubuntu1 [9676 B] Get:54 http://ftpmaster.internal/ubuntu groovy/main armhf libext2fs2 armhf 1.45.6-1ubuntu1 [170 kB] Get:55 http://ftpmaster.internal/ubuntu groovy/main armhf e2fsprogs armhf 1.45.6-1ubuntu1 [510 kB] Get:56 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf passwd armhf 1:4.8.1-1ubuntu6 [749 kB] Get:57 http://ftpmaster.internal/ubuntu groovy/main armhf libcom-err2 armhf 1.45.6-1ubuntu1 [8708 B] Get:58 http://ftpmaster.internal/ubuntu groovy/main armhf libprocps8 armhf 2:3.3.16-4ubuntu1 [29.9 kB] Get:59 http://ftpmaster.internal/ubuntu groovy/main armhf libss2 armhf 1.45.6-1ubuntu1 [9384 B] Get:60 http://ftpmaster.internal/ubuntu groovy/main armhf procps armhf 2:3.3.16-4ubuntu1 [222 kB] Get:61 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libsqlite3-0 armhf 3.32.1-1 [469 kB] Get:62 http://ftpmaster.internal/ubuntu groovy/main armhf tzdata all 2020a-0ubuntu1 [293 kB] Get:63 http://ftpmaster.internal/ubuntu groovy/main armhf libctf0 armhf 2.34-7ubuntu1 [37.1 kB] Get:64 http://ftpmaster.internal/ubuntu groovy/main armhf binutils-arm-linux-gnueabihf armhf 2.34-7ubuntu1 [2093 kB] Get:65 http://ftpmaster.internal/ubuntu groovy/main armhf libbinutils armhf 2.34-7ubuntu1 [317 kB] Get:66 http://ftpmaster.internal/ubuntu groovy/main armhf binutils armhf 2.34-7ubuntu1 [3364 B] Get:67 http://ftpmaster.internal/ubuntu groovy/main armhf binutils-common armhf 2.34-7ubuntu1 [207 kB] Get:68 http://ftpmaster.internal/ubuntu groovy/main armhf libctf-nobfd0 armhf 2.34-7ubuntu1 [38.0 kB] Get:69 http://ftpmaster.internal/ubuntu groovy/main armhf libasan5 armhf 9.3.0-13ubuntu1 [387 kB] Get:70 http://ftpmaster.internal/ubuntu groovy/main armhf g++-9 armhf 9.3.0-13ubuntu1 [6688 kB] Get:71 http://ftpmaster.internal/ubuntu groovy/main armhf gcc-9 armhf 9.3.0-13ubuntu1 [6554 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main armhf libstdc++-9-dev armhf 9.3.0-13ubuntu1 [1782 kB] Get:73 http://ftpmaster.internal/ubuntu groovy/main armhf libgcc-9-dev armhf 9.3.0-13ubuntu1 [687 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main armhf cpp-9 armhf 9.3.0-13ubuntu1 [5882 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main armhf gcc-9-base armhf 9.3.0-13ubuntu1 [19.6 kB] Get:76 http://ftpmaster.internal/ubuntu groovy/main armhf gpg armhf 2.2.20-1ubuntu1 [427 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main armhf gpgconf armhf 2.2.20-1ubuntu1 [107 kB] Get:78 http://ftpmaster.internal/ubuntu groovy/main armhf gpg-agent armhf 2.2.20-1ubuntu1 [195 kB] Get:79 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf linux-libc-dev armhf 5.4.0-33.37 [1078 kB] Get:80 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf make armhf 4.3-1 [156 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.4 MB in 2s (28.0 MB/s) (Reading database ... 12562 files and directories currently installed.) 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Setting up binutils (2.34-7ubuntu1) ... Setting up libgcc-9-dev:armhf (9.3.0-13ubuntu1) ... Setting up gcc-9 (9.3.0-13ubuntu1) ... Setting up libstdc++-9-dev:armhf (9.3.0-13ubuntu1) ... Setting up g++-9 (9.3.0-13ubuntu1) ... Setting up systemd-timesyncd (245.5-3ubuntu1) ... Setting up systemd (245.5-3ubuntu1) ... Initializing machine ID from KVM UUID. Setting up systemd-sysv (245.5-3ubuntu1) ... Processing triggers for libc-bin (2.31-0ubuntu9) ... RUN: /usr/share/launchpad-buildd/bin/sbuild-package PACKAGEBUILD-19389663 armhf groovy-proposed -c chroot:build-PACKAGEBUILD-19389663 --arch=armhf --dist=groovy-proposed --nolog freebayes_1.3.2-3.dsc Initiating build PACKAGEBUILD-19389663 with 4 jobs across 4 processor cores. Kernel reported to sbuild: 4.4.0-177-generic #207-Ubuntu SMP Mon Mar 16 01:17:51 UTC 2020 armv7l sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on bos02-arm64-070.buildd +==============================================================================+ | freebayes 1.3.2-3 (armhf) 01 Jun 2020 11:13 | +==============================================================================+ Package: freebayes Version: 1.3.2-3 Source Version: 1.3.2-3 Distribution: groovy-proposed Machine Architecture: arm64 Host Architecture: armhf Build Architecture: armhf I: NOTICE: Log filtering will replace 'build/freebayes-zLntEC/freebayes-1.3.2' with '<>' I: NOTICE: Log filtering will replace 'build/freebayes-zLntEC' with '<>' I: NOTICE: Log filtering will replace 'home/buildd/build-PACKAGEBUILD-19389663/chroot-autobuild' with '<>' +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Local sources ------------- freebayes_1.3.2-3.dsc exists in .; copying to chroot Check architectures ------------------- Check dependencies ------------------ Merged Build-Depends: build-essential, fakeroot Filtered Build-Depends: build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<>/resolver-o9RdI6/apt_archive/sbuild-build-depends-core-dummy.deb'. Ign:1 copy:/<>/resolver-o9RdI6/apt_archive ./ InRelease Get:2 copy:/<>/resolver-o9RdI6/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-o9RdI6/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-o9RdI6/apt_archive ./ Sources [214 B] Get:5 copy:/<>/resolver-o9RdI6/apt_archive ./ Packages [526 B] Fetched 2859 B in 0s (86.4 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 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 852 B of archives. After this operation, 0 B of additional disk space will be used. Get:1 copy:/<>/resolver-o9RdI6/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 852 B in 0s (73.6 kB/s) Selecting previously unselected package sbuild-build-depends-core-dummy. (Reading database ... 12570 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) ... Merged Build-Depends: debhelper-compat (= 13), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) Filtered Build-Depends: debhelper-compat (= 13), cmake, pkg-config, python3, zlib1g-dev, libbamtools-dev, libvcflib-dev (>= 1.0.0~rc2+dfsg-3~), libtabixpp-dev, libseqlib-dev (>= 1.1.2+dfsg-5), bc, samtools, parallel, libvcflib-tools (>= 1.0.0~rc1+dfsg1-6) dpkg-deb: building package 'sbuild-build-depends-freebayes-dummy' in '/<>/resolver-t5UeNL/apt_archive/sbuild-build-depends-freebayes-dummy.deb'. Ign:1 copy:/<>/resolver-t5UeNL/apt_archive ./ InRelease Get:2 copy:/<>/resolver-t5UeNL/apt_archive ./ Release [2119 B] Ign:3 copy:/<>/resolver-t5UeNL/apt_archive ./ Release.gpg Get:4 copy:/<>/resolver-t5UeNL/apt_archive ./ Sources [331 B] Get:5 copy:/<>/resolver-t5UeNL/apt_archive ./ Packages [640 B] Fetched 3090 B in 0s (86.0 kB/s) Reading package lists... Reading package lists... +------------------------------------------------------------------------------+ | Install freebayes build dependencies (apt-based resolver) | +------------------------------------------------------------------------------+ Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice6 libicu66 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib1 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 man-db mime-support parallel pkg-config po-debconf python3 python3-minimal python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr samtools sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation cmake-doc ninja-build dh-make gettext-doc libasprintf-dev libgettextpo-dev groff lrzip libbamtools-doc krb5-doc krb5-user liblzma-doc lm-sensors tcl8.6 tk8.6 libtool-doc gfortran | fortran95-compiler gcj-jdk r-cran-pracma m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk python3-venv python3.8-venv python3.8-doc binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-cran-covr r-cran-htmlwidgets r-cran-knitr r-cran-rmarkdown r-cran-prettycode r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-jpeg r-cran-viridis r-cran-unitizer r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats r-cran-stringr r-cran-magick r-cran-getopt r-cran-bitops r-cran-doparallel r-cran-foreach r-cran-iterators r-cran-itertools r-cran-curl r-cran-inline r-cran-mockr r-cran-dichromat r-cran-devtools r-cran-usethis r-cran-bit64 r-cran-blob r-cran-hms r-cran-htmltools r-cran-purrr r-cran-tidyr r-cran-zeallot isag Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev libmail-sendmail-perl r-recommended r-base-dev r-doc-html r-cran-cliapp r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-vdiffr r-cran-lubridate r-cran-domc r-cran-abind r-cran-codetools r-cran-curl r-cran-rmarkdown r-cran-bit64 r-cran-hms r-cran-xml2 r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-generics r-cran-dbi cwltool cron | cron-daemon libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: autoconf automake autopoint autotools-dev bc bsdmainutils cmake cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file fontconfig fontconfig-config fonts-dejavu-core gettext gettext-base groff-base intltool-debian libarchive-zip-perl libarchive13 libasn1-8-heimdal libbamtools-dev libbamtools2.5.1 libblas3 libbrotli1 libbsd0 libbwa-dev libcairo2 libcroco3 libcurl3-gnutls libcurl4 libdatrie1 libdebhelper-perl libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1 libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libfml-dev libfml0 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgraphite2-3 libgssapi-krb5-2 libgssapi3-heimdal libharfbuzz0b libhcrypto4-heimdal libheimbase1-heimdal libheimntlm0-heimdal libhts-dev libhts3 libhx509-5-heimdal libice6 libicu66 libjbig0 libjpeg-turbo8 libjpeg8 libjsoncpp-dev libjsoncpp1 libk5crypto3 libkeyutils1 libkrb5-26-heimdal libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common liblzma-dev libmagic-mgc libmagic1 libmpdec2 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpipeline1 libpixman-1-0 libpsl5 libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librhash0 libroken18-heimdal librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libseqlib-dev libseqlib1 libsigsegv2 libsm6 libsmithwaterman-dev libsmithwaterman0 libssh-4 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libtool libuchardet0 libuv1 libvcflib-dev libvcflib-tools libvcflib1 libwebp6 libwind0-heimdal libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxss1 libxt6 littler m4 man-db mime-support parallel pkg-config po-debconf python3 python3-minimal python3.8 python3.8-minimal r-base-core r-cran-assertthat r-cran-backports r-cran-callr r-cran-cli r-cran-colorspace r-cran-crayon r-cran-desc r-cran-digest r-cran-ellipsis r-cran-evaluate r-cran-fansi r-cran-farver r-cran-ggplot2 r-cran-glue r-cran-gridbase r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice r-cran-lifecycle r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgbuild r-cran-pkgconfig r-cran-pkgkitten r-cran-pkgload r-cran-plyr r-cran-praise r-cran-prettyunits r-cran-processx r-cran-ps r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-rlang r-cran-rprojroot r-cran-rstudioapi r-cran-scales r-cran-testthat r-cran-tibble r-cran-utf8 r-cran-vctrs r-cran-viridislite r-cran-withr samtools sbuild-build-depends-freebayes-dummy sysstat ucf unzip x11-common xdg-utils zip zlib1g-dev 0 upgraded, 207 newly installed, 0 to remove and 0 not upgraded. Need to get 96.3 MB of archives. After this operation, 238 MB of additional disk space will be used. Get:1 copy:/<>/resolver-t5UeNL/apt_archive ./ sbuild-build-depends-freebayes-dummy 0.invalid.0 [968 B] Get:2 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3.8-minimal armhf 3.8.3-1 [705 kB] Get:3 http://ftpmaster.internal/ubuntu groovy/main armhf libexpat1 armhf 2.2.9-1build1 [53.3 kB] Get:4 http://ftpmaster.internal/ubuntu groovy/main armhf python3.8-minimal armhf 3.8.3-1 [1582 kB] Get:5 http://ftpmaster.internal/ubuntu groovy/main armhf python3-minimal armhf 3.8.2-0ubuntu2 [23.6 kB] Get:6 http://ftpmaster.internal/ubuntu groovy/main armhf mime-support all 3.64ubuntu1 [30.6 kB] Get:7 http://ftpmaster.internal/ubuntu groovy/main armhf libmpdec2 armhf 2.4.2-3 [66.8 kB] Get:8 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3.8-stdlib armhf 3.8.3-1 [1596 kB] Get:9 http://ftpmaster.internal/ubuntu groovy/main armhf python3.8 armhf 3.8.3-1 [369 kB] Get:10 http://ftpmaster.internal/ubuntu groovy/main armhf libpython3-stdlib armhf 3.8.2-0ubuntu2 [7068 B] Get:11 http://ftpmaster.internal/ubuntu groovy/main armhf python3 armhf 3.8.2-0ubuntu2 [47.6 kB] Get:12 http://ftpmaster.internal/ubuntu groovy/main armhf libbsd0 armhf 0.10.0-1 [49.8 kB] Get:13 http://ftpmaster.internal/ubuntu groovy/main armhf bsdmainutils armhf 11.1.2ubuntu3 [176 kB] Get:14 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB] Get:15 http://ftpmaster.internal/ubuntu groovy/main armhf groff-base armhf 1.22.4-5 [759 kB] Get:16 http://ftpmaster.internal/ubuntu groovy/main armhf libpipeline1 armhf 1.5.2-2build1 [23.5 kB] Get:17 http://ftpmaster.internal/ubuntu groovy/main armhf man-db armhf 2.9.1-1 [1077 kB] Get:18 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic-mgc armhf 1:5.38-5 [218 kB] Get:19 http://ftpmaster.internal/ubuntu groovy/main armhf libmagic1 armhf 1:5.38-5 [68.4 kB] Get:20 http://ftpmaster.internal/ubuntu groovy/main armhf file armhf 1:5.38-5 [22.4 kB] Get:21 http://ftpmaster.internal/ubuntu groovy/main armhf libelf1 armhf 0.176-1.1build1 [41.3 kB] Get:22 http://ftpmaster.internal/ubuntu groovy/main armhf libfribidi0 armhf 1.0.8-2 [21.8 kB] Get:23 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libglib2.0-0 armhf 2.64.3-1 [1124 kB] Get:24 http://ftpmaster.internal/ubuntu groovy/main armhf libicu66 armhf 66.1-2ubuntu2 [8222 kB] Get:25 http://ftpmaster.internal/ubuntu groovy/main armhf libxml2 armhf 2.9.10+dfsg-5 [546 kB] Get:26 http://ftpmaster.internal/ubuntu groovy/main armhf ucf all 3.0042 [56.0 kB] Get:27 http://ftpmaster.internal/ubuntu groovy/main armhf gettext-base armhf 0.19.8.1-10build1 [46.0 kB] Get:28 http://ftpmaster.internal/ubuntu groovy/main armhf libkrb5support0 armhf 1.17-6ubuntu4 [28.0 kB] Get:29 http://ftpmaster.internal/ubuntu groovy/main armhf libk5crypto3 armhf 1.17-6ubuntu4 [79.4 kB] Get:30 http://ftpmaster.internal/ubuntu groovy/main armhf libkeyutils1 armhf 1.6.1-2ubuntu1 [9028 B] Get:31 http://ftpmaster.internal/ubuntu groovy/main armhf libkrb5-3 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[13.1 kB] Get:42 http://ftpmaster.internal/ubuntu groovy/main armhf m4 armhf 1.4.18-4 [187 kB] Get:43 http://ftpmaster.internal/ubuntu groovy/main armhf autoconf all 2.69-11.1 [321 kB] Get:44 http://ftpmaster.internal/ubuntu groovy/main armhf autotools-dev all 20180224.1 [39.6 kB] Get:45 http://ftpmaster.internal/ubuntu groovy/main armhf automake all 1:1.16.2-1ubuntu1 [521 kB] Get:46 http://ftpmaster.internal/ubuntu groovy/main armhf autopoint all 0.19.8.1-10build1 [412 kB] Get:47 http://ftpmaster.internal/ubuntu groovy/main armhf bc armhf 1.07.1-2build1 [81.2 kB] Get:48 http://ftpmaster.internal/ubuntu groovy/main armhf cmake-data all 3.16.3-3ubuntu1 [1612 kB] Get:49 http://ftpmaster.internal/ubuntu groovy/main armhf libarchive13 armhf 3.4.2-1 [292 kB] Get:50 http://ftpmaster.internal/ubuntu groovy/main armhf libbrotli1 armhf 1.0.7-6.1 [269 kB] Get:51 http://ftpmaster.internal/ubuntu groovy/main armhf libroken18-heimdal armhf 7.7.0+dfsg-2 [34.5 kB] Get:52 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http://ftpmaster.internal/ubuntu groovy/main armhf libtool all 2.4.6-14 [161 kB] Get:72 http://ftpmaster.internal/ubuntu groovy/main armhf dh-autoreconf all 19 [16.1 kB] Get:73 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf libdebhelper-perl all 13.1ubuntu1 [64.0 kB] Get:74 http://ftpmaster.internal/ubuntu groovy/main armhf libarchive-zip-perl all 1.68-1 [90.2 kB] Get:75 http://ftpmaster.internal/ubuntu groovy/main armhf libsub-override-perl all 0.09-2 [9532 B] Get:76 http://ftpmaster.internal/ubuntu groovy/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [17.1 kB] Get:77 http://ftpmaster.internal/ubuntu groovy/main armhf dh-strip-nondeterminism all 1.8.1-1 [5232 B] Get:78 http://ftpmaster.internal/ubuntu groovy/main armhf dwz armhf 0.13-5 [153 kB] Get:79 http://ftpmaster.internal/ubuntu groovy/main armhf libcroco3 armhf 0.6.13-1 [70.5 kB] Get:80 http://ftpmaster.internal/ubuntu groovy/main armhf gettext armhf 0.19.8.1-10build1 [835 kB] Get:81 http://ftpmaster.internal/ubuntu groovy/main armhf intltool-debian all 0.35.0+20060710.5 [24.9 kB] Get:82 http://ftpmaster.internal/ubuntu groovy/main armhf po-debconf all 1.0.21 [233 kB] Get:83 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf debhelper all 13.1ubuntu1 [885 kB] Get:84 http://ftpmaster.internal/ubuntu groovy/main armhf libfreetype6 armhf 2.10.1-2 [283 kB] Get:85 http://ftpmaster.internal/ubuntu groovy-proposed/main armhf fonts-dejavu-core all 2.37-2 [1041 kB] Get:86 http://ftpmaster.internal/ubuntu groovy/main armhf fontconfig-config all 2.13.1-2ubuntu3 [28.8 kB] Get:87 http://ftpmaster.internal/ubuntu groovy/main armhf libfontconfig1 armhf 2.13.1-2ubuntu3 [96.1 kB] Get:88 http://ftpmaster.internal/ubuntu groovy/main armhf fontconfig armhf 2.13.1-2ubuntu3 [170 kB] Get:89 http://ftpmaster.internal/ubuntu groovy/universe armhf libbamtools2.5.1 armhf 2.5.1+dfsg-7 [137 kB] Get:90 http://ftpmaster.internal/ubuntu groovy/universe armhf libbamtools-dev armhf 2.5.1+dfsg-7 [194 kB] Get:91 http://ftpmaster.internal/ubuntu groovy/main armhf libblas3 armhf 3.9.0-2 [102 kB] Get:92 http://ftpmaster.internal/ubuntu groovy/universe armhf libbwa-dev armhf 0.7.17-5 [127 kB] Get:93 http://ftpmaster.internal/ubuntu groovy/main armhf libpixman-1-0 armhf 0.38.4-0ubuntu1 [159 kB] Get:94 http://ftpmaster.internal/ubuntu groovy/main armhf libxcb-render0 armhf 1.14-2 [14.2 kB] Get:95 http://ftpmaster.internal/ubuntu groovy/main armhf libxcb-shm0 armhf 1.14-2 [5540 B] Get:96 http://ftpmaster.internal/ubuntu groovy/main armhf libxrender1 armhf 1:0.9.10-1 [15.6 kB] Get:97 http://ftpmaster.internal/ubuntu groovy/main armhf libcairo2 armhf 1.16.0-4ubuntu1 [503 kB] Get:98 http://ftpmaster.internal/ubuntu groovy/main armhf libcurl3-gnutls armhf 7.68.0-1ubuntu2 [200 kB] Get:99 http://ftpmaster.internal/ubuntu groovy/main armhf libdatrie1 armhf 0.2.12-3 [15.2 kB] Get:100 http://ftpmaster.internal/ubuntu groovy/universe armhf libdeflate0 armhf 1.6-1 [46.1 kB] Get:101 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all 1.1.3-2ubuntu1 [61.6 kB] Get:150 http://ftpmaster.internal/ubuntu groovy/main armhf libxt6 armhf 1:1.1.5-1 [129 kB] Get:151 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-base-core armhf 4.0.0.20200528-1 [24.7 MB] Get:152 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-littler armhf 0.3.9-1build1 [297 kB] Get:153 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf littler all 0.3.9-1build1 [2496 B] Get:154 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-pkgkitten all 0.1.5-2 [22.6 kB] Get:155 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-rcpp armhf 1.0.4.6-1build1 [1849 kB] Get:156 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-plyr armhf 1.8.6-2build1 [828 kB] Get:157 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-digest armhf 0.6.25-1build1 [168 kB] Get:158 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-glue 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groovy-proposed/universe armhf r-cran-rcolorbrewer all 1.1-2-3 [54.6 kB] Get:194 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-viridislite all 0.3.0-4 [58.9 kB] Get:195 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-scales all 1.1.1-1build1 [486 kB] Get:196 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-utf8 armhf 1.1.4-1build2 [127 kB] Get:197 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-vctrs armhf 0.3.0-2build1 [912 kB] Get:198 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-pillar all 1.4.4-2build1 [229 kB] Get:199 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] Get:200 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-tibble armhf 3.0.1-1build1 [418 kB] Get:201 http://ftpmaster.internal/ubuntu groovy-proposed/universe armhf r-cran-ggplot2 all 3.3.0+dfsg-2build1 [3069 kB] Get:202 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Setting up libgraphite2-3:armhf (1.3.14-1) ... Setting up libdisorder0:armhf (0.0.2+git20130809.8062ee1-1) ... Setting up libpixman-1-0:armhf (0.38.4-0ubuntu1) ... Setting up libxau6:armhf (1:1.0.9-0ubuntu1) ... Setting up libkeyutils1:armhf (1.6.1-2ubuntu1) ... Setting up libpsl5:armhf (0.21.0-1ubuntu1) ... Setting up mime-support (3.64ubuntu1) ... Setting up libdatrie1:armhf (0.2.12-3) ... Setting up libmagic-mgc (1:5.38-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:armhf (2.64.3-1) ... No schema files found: doing nothing. Setting up libicu66:armhf (66.1-2ubuntu2) ... Setting up unzip (6.0-25ubuntu1) ... Setting up libdebhelper-perl (13.1ubuntu1) ... Setting up libbrotli1:armhf (1.0.7-6.1) ... Setting up x11-common (1:7.7+19ubuntu14) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-2ubuntu1) ... Setting up libsmithwaterman0 (0.0+git20160702.2610e25-8) ... Setting up libnghttp2-14:armhf (1.40.0-1build1) ... Setting up libmagic1:armhf (1:5.38-5) ... Setting up libdeflate0:armhf (1.6-1) ... Setting up bc (1.07.1-2build1) ... Setting up gettext-base (0.19.8.1-10build1) ... Setting up file (1:5.38-5) ... Setting up libldap-common (2.4.49+dfsg-2ubuntu2) ... Setting up libfml0:armhf (0.1-13) ... Setting up libfastahack0 (1.0.0+dfsg-5build1) ... Setting up libjbig0:armhf (2.1-3.1build1) ... Setting up libkrb5support0:armhf (1.17-6ubuntu4) ... Setting up libsasl2-modules-db:armhf (2.1.27+dfsg-2) ... Setting up libfastahack-dev (1.0.0+dfsg-5build1) ... Setting up zip (3.0-11build1) ... Setting up autotools-dev (20180224.1) ... 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WARNING: tempfile is deprecated; consider using mktemp instead. Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /lib/systemd/system/sysstat.service. Setting up xdg-utils (1.1.3-2ubuntu1) ... Setting up libjsoncpp1:armhf (1.7.4-3.1ubuntu2) ... Setting up libpython3-stdlib:armhf (3.8.2-0ubuntu2) ... Setting up libheimbase1-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libjpeg8:armhf (8c-2ubuntu8) ... Setting up libfile-stripnondeterminism-perl (1.8.1-1) ... Setting up libpaper1:armhf (1.1.28) ... Creating config file /etc/papersize with new version Setting up libice6:armhf (2:1.0.10-0ubuntu1) ... Setting up libjsoncpp-dev:armhf (1.7.4-3.1ubuntu2) ... Setting up libxdmcp6:armhf (1:1.1.3-0ubuntu1) ... 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Setting up bsdmainutils (11.1.2ubuntu3) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-6ubuntu4) ... Setting up libcroco3:armhf (0.6.13-1) ... Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-8) ... Setting up parallel (20161222-1.1) ... Setting up libssh-4:armhf (0.9.4-1ubuntu1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.1-1) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up libx11-6:armhf (2:1.6.9-2ubuntu1) ... Setting up libtiff5:armhf (4.1.0+git191117-2build1) ... Setting up libfontconfig1:armhf (2.13.1-2ubuntu3) ... Setting up libsm6:armhf (2:1.2.3-1) ... Setting up automake (1:1.16.2-1ubuntu1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up fontconfig (2.13.1-2ubuntu3) ... Regenerating fonts cache... done. Setting up gettext (0.19.8.1-10build1) ... Setting up libxrender1:armhf (1:0.9.10-1) ... Setting up libhx509-5-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libpango-1.0-0:armhf (1.44.7-2ubuntu4) ... Setting up libxext6:armhf (2:1.3.4-0ubuntu1) ... Setting up man-db (2.9.1-1) ... 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 libcairo2:armhf (1.16.0-4ubuntu1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxt6:armhf (1:1.1.5-1) ... Setting up libxss1:armhf (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:armhf (1.44.7-2ubuntu4) ... Setting up libpangocairo-1.0-0:armhf (1.44.7-2ubuntu4) ... Setting up libkrb5-26-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libxft2:armhf (2.3.3-0ubuntu1) ... Setting up po-debconf (1.0.21) ... Setting up libtk8.6:armhf (8.6.10-1) ... Setting up libheimntlm0-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libgssapi3-heimdal:armhf (7.7.0+dfsg-2) ... Setting up libldap-2.4-2:armhf (2.4.49+dfsg-2ubuntu2) ... Setting up libcurl3-gnutls:armhf (7.68.0-1ubuntu2) ... Setting up libcurl4:armhf (7.68.0-1ubuntu2) ... Setting up libhts3:armhf (1.10.2-3) ... Setting up libseqlib1 (1.1.2+dfsg-6) ... Setting up libhts-dev:armhf (1.10.2-3) ... Setting up libseqlib-dev (1.1.2+dfsg-6) ... Setting up samtools (1.10-3) ... Setting up r-base-core (4.0.0.20200528-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.3.4-4ubuntu2) ... Setting up r-cran-gtable (0.3.0+dfsg-2build1) ... Setting up r-cran-labeling (0.3-4build1) ... Setting up r-cran-lattice (0.20-41-1build1) ... Setting up r-cran-ps (1.3.3-1build1) ... 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Processing triggers for systemd (245.5-3ubuntu1) ... +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.4.0-177-generic arm64 (armv7l) Toolchain package versions: binutils_2.34-7ubuntu1 dpkg-dev_1.19.7ubuntu3 g++-9_9.3.0-13ubuntu1 gcc-9_9.3.0-13ubuntu1 libc6-dev_2.31-0ubuntu9 libstdc++-9-dev_9.3.0-13ubuntu1 libstdc++6_10.1.0-3ubuntu1 linux-libc-dev_5.4.0-33.37 Package versions: adduser_3.118ubuntu2 advancecomp_2.1-2.1build1 apt_2.1.5 autoconf_2.69-11.1 automake_1:1.16.2-1ubuntu1 autopoint_0.19.8.1-10build1 autotools-dev_20180224.1 base-files_11ubuntu7 base-passwd_3.5.47 bash_5.0-6ubuntu1 bc_1.07.1-2build1 binutils_2.34-7ubuntu1 binutils-arm-linux-gnueabihf_2.34-7ubuntu1 binutils-common_2.34-7ubuntu1 bsdmainutils_11.1.2ubuntu3 bsdutils_1:2.35.1-5ubuntu2 build-essential_12.8ubuntu1 bzip2_1.0.8-3 ca-certificates_20190110ubuntu1 cmake_3.16.3-3ubuntu1 cmake-data_3.16.3-3ubuntu1 coreutils_8.30-3ubuntu2 cpp_4:9.3.0-1ubuntu2 cpp-9_9.3.0-13ubuntu1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1ubuntu1 debianutils_4.11 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dpkg_1.19.7ubuntu3 dpkg-dev_1.19.7ubuntu3 dwz_0.13-5 e2fsprogs_1.45.6-1ubuntu1 fakeroot_1.24-1 fdisk_2.35.1-5ubuntu2 file_1:5.38-5 findutils_4.7.0-1ubuntu1 fontconfig_2.13.1-2ubuntu3 fontconfig-config_2.13.1-2ubuntu3 fonts-dejavu-core_2.37-2 g++_4:9.3.0-1ubuntu2 g++-9_9.3.0-13ubuntu1 gcc_4:9.3.0-1ubuntu2 gcc-10-base_10.1.0-3ubuntu1 gcc-9_9.3.0-13ubuntu1 gcc-9-base_9.3.0-13ubuntu1 gettext_0.19.8.1-10build1 gettext-base_0.19.8.1-10build1 gpg_2.2.20-1ubuntu1 gpg-agent_2.2.20-1ubuntu1 gpgconf_2.2.20-1ubuntu1 gpgv_2.2.20-1ubuntu1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2ubuntu1 hostname_3.23 init_1.57 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapparmor1_2.13.3-7ubuntu6 libapt-pkg6.0_2.1.5 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r-cran-prettyunits_1.1.1-2build1 r-cran-processx_3.4.2-1build1 r-cran-ps_1.3.3-1build1 r-cran-r6_2.4.1-2build1 r-cran-rcolorbrewer_1.1-2-3 r-cran-rcpp_1.0.4.6-1build1 r-cran-rlang_0.4.6-1build1 r-cran-rprojroot_1.3-2-3build1 r-cran-rstudioapi_0.11-2 r-cran-scales_1.1.1-1build1 r-cran-testthat_2.3.2-2build1 r-cran-tibble_3.0.1-1build1 r-cran-utf8_1.1.4-1build2 r-cran-vctrs_0.3.0-2build1 r-cran-viridislite_0.3.0-4 r-cran-withr_2.2.0-2 readline-common_8.0-4 samtools_1.10-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-freebayes-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysstat_12.3.2-1 systemd_245.5-3ubuntu1 systemd-sysv_245.5-3ubuntu1 systemd-timesyncd_245.5-3ubuntu1 sysvinit-utils_2.96-3ubuntu1 tar_1.30+dfsg-7 tzdata_2020a-0ubuntu1 ubuntu-keyring_2020.02.11.2 ucf_3.0042 unzip_6.0-25ubuntu1 util-linux_2.35.1-5ubuntu2 x11-common_1:7.7+19ubuntu14 xdg-utils_1.1.3-2ubuntu1 xz-utils_5.2.4-1 zip_3.0-11build1 zlib1g_1:1.2.11.dfsg-2ubuntu1 zlib1g-dev_1:1.2.11.dfsg-2ubuntu1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- gpgv: Signature made Mon Jun 1 07:31:39 2020 UTC gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./freebayes_1.3.2-3.dsc dpkg-source: info: extracting freebayes in freebayes-1.3.2 dpkg-source: info: unpacking freebayes_1.3.2.orig.tar.gz dpkg-source: info: unpacking freebayes_1.3.2-3.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying use_debian_libs.patch dpkg-source: info: applying fix_all_target.patch dpkg-source: info: applying fix_test.patch dpkg-source: info: applying vcffirstheader.patch dpkg-source: info: applying skip_failing_test.patch dpkg-source: info: applying 2to3.patch dpkg-source: info: applying 1ad5cd64ac7270aac03d58d2dba0861ecc85b6b6.patch dpkg-source: info: applying hardening dpkg-source: info: applying version_bump Check disc 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-19389663 SCHROOT_CHROOT_NAME=build-PACKAGEBUILD-19389663 SCHROOT_COMMAND=env SCHROOT_GID=2501 SCHROOT_GROUP=buildd SCHROOT_SESSION_ID=build-PACKAGEBUILD-19389663 SCHROOT_UID=2001 SCHROOT_USER=buildd SHELL=/bin/sh TERM=unknown USER=buildd V=1 dpkg-buildpackage ----------------- dpkg-buildpackage: info: source package freebayes dpkg-buildpackage: info: source version 1.3.2-3 dpkg-buildpackage: info: source distribution unstable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf debian/rules clean dh clean --no-parallel dh_auto_clean -O--no-parallel make -j1 clean make[1]: Entering directory '/<>' cd src && make clean make[2]: Entering directory '/<>/src' rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp make[2]: Leaving directory '/<>/src' rm -fr bin/* make[1]: Leaving directory '/<>' dh_autoreconf_clean -O--no-parallel dh_clean -O--no-parallel debian/rules binary-arch dh binary-arch --no-parallel dh_update_autotools_config -a -O--no-parallel dh_autoreconf -a -O--no-parallel dh_auto_configure -a -O--no-parallel debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- CXXFLAGS="-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" make -j1 "INSTALL=install --strip-program=true" "CXXFLAGS=-g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64" make[2]: Entering directory '/<>' cd src && make make[3]: Entering directory '/<>/src' DETECTED_VERSION = v1.3.2 CURRENT_VERSION = Updating version file. g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c freebayes.cpp In file included from /usr/include/c++/9/vector:72, from freebayes.cpp:12: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SampleDataLikelihood&}; _Tp = SampleDataLikelihood; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from freebayes.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In member function ‘void Results::update(SampleDataLikelihoods&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from freebayes.cpp:13: /usr/include/c++/9/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::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, double> >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from freebayes.cpp:12: /usr/include/c++/9/bits/stl_vector.h: In function ‘int main(int, char**)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from freebayes.cpp:13: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, double>, std::_Select1st, double> >, std::less >, std::allocator, double> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, double> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from freebayes.cpp:12: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c BedReader.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c CNV.cpp gcc -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -std=gnu++11 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c fastlz.c cc1: warning: command line option ‘-std=gnu++11’ is valid for C++/ObjC++ but not for C g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Utility.cpp In file included from /usr/include/c++/9/vector:72, from Utility.h:7, from Utility.cpp:3: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/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++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘double entropy(const string&)’: /usr/include/c++/9/bits/vector.tcc:121:4: 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++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Fasta.cpp In file included from /usr/include/c++/9/map:60, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/9/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::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, FastaIndexEntry>; _KeyOfValue = std::_Select1st, FastaIndexEntry> >; _Compare = std::less >; _Alloc = std::allocator, FastaIndexEntry> >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, FastaIndexEntry> >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/9/bits/stl_map.h: In member function ‘std::string FastaReference::sequenceNameStartingWith(std::string)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, FastaIndexEntry> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:72, from Fasta.h:15, from Fasta.cpp:9: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const FastaIndexEntry&}; _Tp = FastaIndexEntry; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_val]’: /usr/include/c++/9/bits/stl_heap.h:128:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 128 | __push_heap(_RandomAccessIterator __first, | ^~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = FastaIndexEntry; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/9/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_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1671 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Fasta.h:12, from Fasta.cpp:9: /usr/include/c++/9/bits/stl_map.h: In function ‘std::ostream& operator<<(std::ostream&, FastaIndex&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, FastaIndexEntry>, std::_Select1st, FastaIndexEntry> >, std::less >, std::allocator, FastaIndexEntry> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, FastaIndexEntry> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from Fasta.h:15, from Fasta.cpp:9: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Fasta.h:18, from Fasta.cpp:9: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Parameters.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Allele.cpp Allele.cpp: In member function ‘const string Allele::base() const’: Allele.cpp:297:1: warning: control reaches end of non-void function [-Wreturn-type] 297 | } | ^ In file included from /usr/include/c++/9/vector:72, from Allele.h:8, from Allele.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from Allele.h:8, from Allele.cpp:1: /usr/include/c++/9/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::vector&, bool (*)(Allele&, Allele&))’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::vector&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘std::vector > groupAlleles_copy(std::__cxx11::list&, bool (*)(Allele&, Allele&))’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘std::vector alleleUnion(std::vector&, std::vector&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from Allele.h:10, from Allele.cpp:1: /usr/include/c++/9/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 = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Allele.h:10, from Allele.cpp:1: /usr/include/c++/9/bits/stl_map.h: In function ‘std::map countAlleles(std::vector&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘std::map countAlleles(std::vector&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘std::map countAlleles(std::__cxx11::list&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from Allele.h:8, from Allele.cpp:1: /usr/include/c++/9/bits/stl_vector.h: In function ‘std::vector uniqueAlleles(std::__cxx11::list&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Sample.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Result.cpp In file included from /usr/include/c++/9/algorithm:62, from Result.h:6, from Result.cpp:1: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Result.h:6, from Result.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Result.h:6, from Result.cpp:1: /usr/include/c++/9/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_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In member function ‘void Result::sortDataLikelihoods()’: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c AlleleParser.cpp In file included from /usr/include/c++/9/vector:72, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In member function ‘void RegisteredAlignment::addAllele(Allele, bool, int, bool)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘void RegisteredAlignment::addAllele(Allele, bool, int, bool)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::iterator) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 184 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Allele}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:340:5: note: parameter passing for argument of type ‘std::vector::const_iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 340 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:356:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 356 | _M_realloc_insert(begin() + __n, std::move(__v)); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h: In function ‘_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred]’: /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 112 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:112:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In function ‘_ForwardIterator std::__remove_if(_ForwardIterator, _ForwardIterator, _Predicate) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_pred]’: /usr/include/c++/9/bits/stl_algo.h:860:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 860 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:860:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:161:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 161 | return __find_if(__first, __last, __pred, | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 162 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from AlleleParser.h:8, from AlleleParser.cpp:1: /usr/include/c++/9/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 = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In member function ‘void RegisteredAlignment::clumpAlleles(bool, int, bool)’: /usr/include/c++/9/bits/stl_algo.h:939:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 939 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 940 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h:939:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 939 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 940 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h:939:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 939 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 940 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/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_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 408 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1671 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In member function ‘bool RegisteredAlignment::fitHaplotype(int, int, Allele*&, bool)’: /usr/include/c++/9/bits/stl_algo.h:939:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 939 | return std::__remove_if(__first, __last, | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 940 | __gnu_cxx::__ops::__pred_iter(__pred)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ^ In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 408 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1671 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from AlleleParser.h:8, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_map.h: In member function ‘std::vector AlleleParser::genotypeAlleles(std::map, std::vector >&, Samples&, bool, int)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_vector.h:1291:57: note: parameter passing for argument of type ‘std::vector::const_iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1291 | { return _M_insert_rval(__position, std::move(__x)); } | ^ In file included from /usr/include/c++/9/algorithm:62, from AlleleParser.h:11, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from AlleleParser.h:7, from AlleleParser.cpp:1: /usr/include/c++/9/bits/stl_vector.h:1291:57: note: parameter passing for argument of type ‘std::vector::const_iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 1291 | { return _M_insert_rval(__position, std::move(__x)); } | ^ /usr/include/c++/9/bits/stl_vector.h: In member function ‘void AlleleParser::updateInputVariants(long int, int)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In member function ‘void AlleleParser::getInputVariantsInRegion(std::string&, long int, long int)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Genotype.cpp In file included from /usr/include/c++/9/vector:72, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {GenotypeElement}; _Tp = GenotypeElement; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Genotype}; _Tp = Genotype; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/vector:67, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_vector.h: In member function ‘std::vector Genotype::alternateAlleles(std::string&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h: In function ‘std::vector > multichoose(int, std::vector&) [with T = Allele]’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/9/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 = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/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 = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 In file included from /usr/include/c++/9/map:61, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_map.h: In function ‘void addAllHomozygousCombos(std::__cxx11::list&, SampleDataLikelihoods&, SampleDataLikelihoods&, SampleDataLikelihoods&, Samples&, std::vector&, long double, bool, bool, bool, bool, bool, bool, long double)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In function ‘void combinePopulationCombos(std::__cxx11::list&, std::map, std::__cxx11::list >&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/map:60, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/9/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 = Allele; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = Allele; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 408 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1671 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘std::vector allPossibleGenotypes(int, std::vector&)’: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:72, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/9/bits/vector.tcc:121:4: 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++/9/bits/vector.tcc:121:4: 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++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/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_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘void sortSampleDataLikelihoods(std::vector&)’: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/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_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsByMarginals(std::vector&)’: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/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_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1671 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsByMarginalsAndObs(std::vector&)’: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = SampleDataLikelihood; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/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_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h: In function ‘bool sortSampleDataLikelihoodsScaledByMarginals(std::vector&)’: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Distance = int; _Tp = std::pair; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h: In function ‘void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 243 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, | ^~~~~~~~~~ /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 /usr/include/c++/9/bits/stl_heap.h:243:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, std::vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 In file included from /usr/include/c++/9/bits/stl_algo.h:61, from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_heap.h:408:19: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 408 | std::__pop_heap(__first, __last, __last, __comp); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1671:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1671 | std::__make_heap(__first, __middle, __comp); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Genotype.h:11, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_map.h: In function ‘std::vector > alternateAlleles(GenotypeCombo&, std::string)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:72, from Genotype.h:6, from Genotype.cpp:1: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/algorithm:62, from Genotype.h:8, from Genotype.cpp:1: /usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c DataLikelihood.cpp In file included from /usr/include/c++/9/vector:72, from DataLikelihood.h:5, from DataLikelihood.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector >::iterator’ {aka ‘__gnu_cxx::__normal_iterator*, std::vector > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {SampleDataLikelihood}; _Tp = SampleDataLikelihood; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 /usr/include/c++/9/bits/vector.tcc: In function ‘std::vector > probObservedAllelesGivenGenotypes(Sample&, std::vector&, Bias&, std::vector&, Contamination&, std::map, double>&, Parameters&)’: /usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator*, std::vector > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In function ‘void calculateSampleDataLikelihoods(Samples&, Results&, AlleleParser*, std::map >&, Parameters&, bool, Bias&, std::vector&, Contamination&, std::map, double>&, std::map, std::vector > >&, std::map, std::vector > >&, std::map, std::vector > >&)’: /usr/include/c++/9/bits/vector.tcc:121:4: 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++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Multinomial.cpp In file included from /usr/include/c++/9/vector:72, from Utility.h:7, from Multinomial.h:4, from Multinomial.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: 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++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Ewens.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c ResultData.cpp In file included from /usr/include/c++/9/vector:72, from ResultData.h:4, from ResultData.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Allele&}; _Tp = Allele; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from Genotype.h:11, from ResultData.h:7, from ResultData.cpp:1: /usr/include/c++/9/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 = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from ResultData.h:4, from ResultData.cpp:1: /usr/include/c++/9/bits/stl_vector.h: In member function ‘vcflib::Variant& Results::vcf(vcflib::Variant&, BigFloat, long double, Samples&, std::string, std::vector&, std::map, int>, int, std::vector >&, int, GenotypeCombo&, std::map, std::vector >&, std::map, std::vector >&, std::map >&, std::map >&, std::vector >&, AlleleParser*)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Genotype.h:11, from ResultData.h:7, from ResultData.cpp:1: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Dirichlet.cpp In file included from /usr/include/c++/9/vector:72, from Dirichlet.h:1, from Dirichlet.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:121:4: 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++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Marginals.cpp In file included from /usr/include/c++/9/vector:72, from Marginals.h:3, from Marginals.cpp:1: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:60, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/9/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 = Genotype*; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/9/bits/stl_map.h: In function ‘long double marginalGenotypeLikelihoods(std::__cxx11::list&, SampleDataLikelihoods&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from Marginals.h:3, from Marginals.cpp:1: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from Marginals.h:3, from Marginals.cpp:1: /usr/include/c++/9/bits/stl_vector.h: In function ‘long double balancedMarginalGenotypeLikelihoods(std::__cxx11::list&, SampleDataLikelihoods&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/include/c++/9/vector:67, from Marginals.h:3, from Marginals.cpp:1: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from Marginals.h:4, from Marginals.cpp:1: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c split.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c LeftAlign.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c IndelAllele.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c Bias.cpp In file included from /usr/include/c++/9/vector:72, from Bias.h:8, from Bias.cpp:4: /usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]’: /usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ {aka ‘__gnu_cxx::__normal_iterator >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/vector:67, from Bias.h:8, from Bias.cpp:4: /usr/include/c++/9/bits/stl_vector.h: In member function ‘void Bias::open(std::string&)’: /usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1195 | _M_realloc_insert(end(), __x); | ^~~~~~~~~~~~~~~~~ g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o Contamination.o Contamination.cpp g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c NonCall.cpp In file included from /usr/include/c++/9/set:60, from NonCall.h:6, from NonCall.cpp:1: /usr/include/c++/9/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::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, NonCall>; _KeyOfValue = std::_Select1st, NonCall> >; _Compare = std::less >; _Alloc = std::allocator, NonCall> >]’: /usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, NonCall> >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/9/map:61, from NonCall.h:7, from NonCall.cpp:1: /usr/include/c++/9/bits/stl_map.h: In member function ‘void NonCalls::aggregatePerSample(std::map, NonCall>&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, NonCall> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/include/c++/9/bits/stl_map.h: In member function ‘void NonCalls::record(const string&, long int, const Samples&)’: /usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, NonCall>, std::_Select1st, NonCall> >, std::less >, std::allocator, NonCall> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, NonCall> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c SegfaultHandler.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp freebayes.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o -o ../bin/freebayes -lz -pthread -lbamtools -ltabixpp -lz -lm -lpthread -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -lseqlib -lbwa -ljsoncpp -lz -pthread g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp -c bamleftalign.cpp g++ -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -D_FILE_OFFSET_BITS=64 -I../ttmath -I/usr/include/bamtools -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/usr/include/SeqLib -I/usr/include/jsoncpp bamleftalign.o BedReader.o CNV.o fastlz.o Fasta.o Parameters.o Allele.o Sample.o Result.o AlleleParser.o Utility.o Genotype.o DataLikelihood.o Multinomial.o Ewens.o ResultData.o Dirichlet.o Marginals.o split.o LeftAlign.o IndelAllele.o Bias.o Contamination.o NonCall.o SegfaultHandler.o -o ../bin/bamleftalign -lz -pthread -lbamtools -ltabixpp -lz -lm -lpthread -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -lseqlib -lbwa -ljsoncpp -lz -pthread make[3]: Leaving directory '/<>/src' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_auto_test make[1]: Entering directory '/<>' mkdir -p /<>/test/bash-tap/ for bt in /<>/debian/bash-tap/* ; do ln -s ${bt} /<>/test/bash-tap/`basename ${bt}` ; done ln -s /<>/debian/test-simple-bash/lib test/test-simple-bash chmod +x vcflib/scripts/vcffirstheader # export PATH=/usr/lib/vcflib/binaries/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test echo "Tests should be run" && PATH=/usr/lib/vcflib/binaries/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games dh_auto_test && echo "Tests were running successfully" Tests should be run make -j1 test make[2]: Entering directory '/<>' cd test && make test make[3]: Entering directory '/<>/test' prove -v t t/00_region_and_target_handling.t .. 1..11 ok 1 - ref:4-5 ref:6-7 are empty ok 2 - ref:4 ref:6 are empty ok 3 - ref:5-6 ref:7-8 ok 4 - ref:5 ref:7 ok 5 - ref:5- ok 6 - full output ok 7 - --targets t/../00_region_and_target_handling.t.bed ok 8 - --region ref ok 9 - ref:1,0- ok 10 - ref:1,0-1,1 ok 11 - region outside of bounds error ok [E::idx_find_and_load] Could not retrieve index file for '-' Random access with SetRegion not available for STDIN reading (no index file) ERROR(freebayes): Could not SetRegion to q:1..10000 t/01_call_variants.t ............... 1..23 ok 1 - variant calling recovers most of the GiAB variants in a test region ok 2 - freebayes produces the same number of calls if targeted per site or called without targets ok 3 - a targets bed file can be used with the same effect as running by region ok 4 - reading from stdin or not makes no difference ok 5 - freebayes processes all alignments in input ok 6 - freebayes correctly handles variant input ok 7 - freebayes puts required variants in output ok 8 - freebayes limits calls to input variants correctly ok 9 - freebayes reports all input variants even when there is no input data ok 10 - freebayes handles region and variant input ok 11 - freebayes limits to variant input correctly when region is given ok 12 - freebayes handles variant input and reading from stdin ok 13 - freebayes limits to variant input when reading from stdin ok 14 - freebayes handles region, stdin, and variant input ok 15 - freebayes bails out when given a gzipped or corrupted reference ok 16 - running in parallel makes no difference ok 17 - freebayes handles region and variant input even with : in contig names ok 18 - freebayes can handle spliced reads ok 19 - freebayes produces the expected number of lines of gVCF output ok 20 - freebayes produces the expected number of lines of gVCF output ok 21 - freebayes produces the expected number of lines of gVCF output ok 22 - the CNV map may be used to specify per-sample copy numbers ok 23 - freebayes makes the expected number of calls when capping coverage ok t/02_multi_bam.t ................... 1..7 ok 1 - freebayes calls from two identical BAMs ok 2 - freebayes calls from two BAMs with different samples for different read groups ok 3 - freebayes calls from two BAMs with different technologies for different read groups ok 4 - freebayes rejects two BAMs with different samples for same read groups ok 5 - freebayes rejects two BAMs with different technologies for same read groups ok 6 - freebayes calls multiple alts from two different BAMs ok 7 - freebayes rejects two BAMs with the same name ok t/03_reference_bases.t ............. 1..3 ok 1 - freebayes rejects invalid reference ok 2 - freebayes does not put uppercase IUPAC bases in VCFs ok 3 - freebayes does not put lowercase IUPAC bases in VCFs ok All tests successful. Files=4, Tests=44, 31 wallclock secs ( 0.08 usr 0.02 sys + 25.18 cusr 12.48 csys = 37.76 CPU) Result: PASS make[3]: Leaving directory '/<>/test' make[2]: Leaving directory '/<>' Tests were running successfully rm -rf /<>/test/bash-tap rm test/test-simple-bash/lib make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a -O--no-parallel dh_prep -a -O--no-parallel debian/rules override_dh_auto_install make[1]: Entering directory '/<>' echo "Skip autoinstall process - files are moved around by dh_install" Skip autoinstall process - files are moved around by dh_install make[1]: Leaving directory '/<>' dh_install -a -O--no-parallel dh_installdocs -a -O--no-parallel dh_installchangelogs -a -O--no-parallel dh_installexamples -a -O--no-parallel dh_installsystemduser -a -O--no-parallel dh_perl -a -O--no-parallel dh_link -a -O--no-parallel dh_strip_nondeterminism -a -O--no-parallel dh_compress -a -O--no-parallel dh_fixperms -a -O--no-parallel dh_missing -a -O--no-parallel dh_dwz -a -a -O--no-parallel dh_strip -a -a -O--no-parallel dh_makeshlibs -a -a -O--no-parallel dh_shlibdeps -a -a -O--no-parallel dpkg-shlibdeps: warning: debian/freebayes/usr/bin/freebayes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/freebayes/usr/bin/bamleftalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a -O--no-parallel dh_gencontrol -a -O--no-parallel dh_md5sums -a -O--no-parallel dh_builddeb -a -O--no-parallel INFO: pkgstriptranslations version 144 INFO: pkgstriptranslations version 144 pkgstriptranslations: processing freebayes (in debian/freebayes); do_strip: , oemstrip: pkgstriptranslations: processing freebayes-dbgsym (in debian/.debhelper/freebayes/dbgsym-root); do_strip: , oemstrip: pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgmaintainermangler: Maintainer field overridden to "Ubuntu Developers " pkgstripfiles: processing control file: debian/freebayes/DEBIAN/control, package freebayes, directory debian/freebayes pkgstripfiles: processing control file: debian/.debhelper/freebayes/dbgsym-root/DEBIAN/control, package freebayes-dbgsym, directory debian/.debhelper/freebayes/dbgsym-root dpkg-deb: building package 'freebayes-dbgsym' in 'debian/.debhelper/scratch-space/build-freebayes/freebayes-dbgsym_1.3.2-3_armhf.deb'. pkgstripfiles: Running PNG optimization (using 4 cpus) for package freebayes ... pkgstripfiles: No PNG files. dpkg-deb: building package 'freebayes' in '../freebayes_1.3.2-3_armhf.deb'. Renaming freebayes-dbgsym_1.3.2-3_armhf.deb to freebayes-dbgsym_1.3.2-3_armhf.ddeb dpkg-genbuildinfo --build=any dpkg-genchanges --build=any -mLaunchpad Build Daemon >../freebayes_1.3.2-3_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 20200601-1121 Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Post Build Chroot | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ freebayes_1.3.2-3_armhf.changes: -------------------------------- Format: 1.8 Date: Mon, 01 Jun 2020 02:50:39 +0530 Source: freebayes Binary: freebayes Architecture: armhf Version: 1.3.2-3 Distribution: groovy-proposed Urgency: medium Maintainer: Launchpad Build Daemon Changed-By: Pranav Ballaney Description: freebayes - Bayesian haplotype-based polymorphism discovery and genotyping Changes: freebayes (1.3.2-3) unstable; urgency=medium . * Team upload . [ Pranav Ballaney ] * Install test data * Add autopkgtests * Install docs and binaries . [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * debhelper-compat 13 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. * Add missing files to debian/source/include-binaries Checksums-Sha1: dbb22bb79d149d35611bfced1742c687225178a8 9368316 freebayes-dbgsym_1.3.2-3_armhf.ddeb 50956ce2e0cf45d7326877b3566309e1a967ae0d 11155 freebayes_1.3.2-3_armhf.buildinfo 731eb23c83a544e14b108055cee69bf5c7aea299 1293772 freebayes_1.3.2-3_armhf.deb Checksums-Sha256: a1c9f41029ee532792b75fae9dd87f3d641a1d972e0e67357d4e5205db881537 9368316 freebayes-dbgsym_1.3.2-3_armhf.ddeb a2c128bf1c62a54d3ed5ba5e918aaa6635b2875985d94469ef4e59611a2c57c2 11155 freebayes_1.3.2-3_armhf.buildinfo 8bc3f52e082e6b3321771c26eeda68c5c325080269df1c5d8efb377b31d66727 1293772 freebayes_1.3.2-3_armhf.deb Files: 1821d20fa1748e84a0264b77c2f879c7 9368316 debug optional freebayes-dbgsym_1.3.2-3_armhf.ddeb 3a06a0b7493e2bffa99646b3c722b7cc 11155 science optional freebayes_1.3.2-3_armhf.buildinfo 3a5a5c64d923e14ae09f11fe709f3a25 1293772 science optional freebayes_1.3.2-3_armhf.deb +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ freebayes_1.3.2-3_armhf.deb --------------------------- new debian package, version 2.0. size 1293772 bytes: control archive=2052 bytes. 931 bytes, 18 lines control 4005 bytes, 48 lines md5sums Package: freebayes Version: 1.3.2-3 Architecture: armhf Maintainer: Ubuntu Developers Original-Maintainer: Debian Med Packaging Team Installed-Size: 3601 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libseqlib1 (>= 1.1.2+dfsg-5), libstdc++6 (>= 9), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.1+dfsg), zlib1g (>= 1:1.1.4) Recommends: parallel Section: science Priority: optional Homepage: https://github.com/ekg/freebayes Description: Bayesian haplotype-based polymorphism discovery and genotyping FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. drwxr-xr-x root/root 0 2020-05-31 21:20 ./ drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/ drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/bin/ -rwxr-xr-x root/root 1458696 2020-05-31 21:20 ./usr/bin/bamleftalign -rwxr-xr-x root/root 1483160 2020-05-31 21:20 ./usr/bin/freebayes drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/share/ drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-05-31 21:20 ./usr/share/doc/freebayes/ -rw-r--r-- root/root 9516 2019-10-06 08:14 ./usr/share/doc/freebayes/README.md.gz -rw-r--r-- root/root 278 2020-05-31 21:20 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+------------------------------------------------------------------------------+ Purging /<> Not removing build depends: as requested +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: armhf Build-Space: 118652 Build-Time: 402 Distribution: groovy-proposed Host Architecture: armhf Install-Time: 57 Job: freebayes_1.3.2-3.dsc Machine Architecture: arm64 Package: freebayes Package-Time: 461 Source-Version: 1.3.2-3 Space: 118652 Status: successful Version: 1.3.2-3 -------------------------------------------------------------------------------- Finished at 20200601-1121 Build needed 00:07:41, 118652k disc space RUN: /usr/share/launchpad-buildd/bin/in-target scan-for-processes --backend=chroot --series=groovy --arch=armhf PACKAGEBUILD-19389663 Scanning for processes to kill in build PACKAGEBUILD-19389663