sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | stacks 2.53+dfsg-1 (armel) Wed, 06 May 2020 21:00:32 +0000 | +==============================================================================+ Package: stacks Version: 2.53+dfsg-1 Source Version: 2.53+dfsg-1 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-97963314-486d-49a7-8fb1-a2cc8f817081' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-ZLtHDw/resolver-OgpMB7' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [146 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-06-0810.29.pdiff [16.1 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-06-1409.59.pdiff [25.9 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-06-2009.26.pdiff [8015 B] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-06-0810.29.pdiff [21.3 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-06-1409.59.pdiff [35.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-06-2009.26.pdiff [5329 B] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-05-06-2009.26.pdiff [8015 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-05-06-2009.26.pdiff [5329 B] Get:10 http://debian.oregonstate.edu/debian unstable/main armel Packages [7906 kB] Fetched 8220 kB in 1s (5542 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils fdisk libblkid1 libfdisk1 libmount1 libsmartcols1 libuuid1 mount util-linux 9 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2473 kB of archives. After this operation, 14.3 kB of additional disk space will be used. Get:1 http://debian.oregonstate.edu/debian unstable/main amd64 bsdutils amd64 1:2.35.1-2 [143 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libblkid1 amd64 2.35.1-2 [190 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libuuid1 amd64 2.35.1-2 [78.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libfdisk1 amd64 2.35.1-2 [230 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 libmount1 amd64 2.35.1-2 [206 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libsmartcols1 amd64 2.35.1-2 [153 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 fdisk amd64 2.35.1-2 [182 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 util-linux amd64 2.35.1-2 [1113 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 mount amd64 2.35.1-2 [178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2473 kB in 0s (72.1 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12638 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.35.1-2_amd64.deb ... Unpacking bsdutils (1:2.35.1-2) over (1:2.35.1-1) ... Setting up bsdutils (1:2.35.1-2) ... (Reading database ... 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Processing triggers for libc-bin (2.30-7) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'stacks' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/stacks.git Please use: git clone https://salsa.debian.org/med-team/stacks.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 331 kB of source archives. Get:1 http://debian.oregonstate.edu/debian unstable/main stacks 2.53+dfsg-1 (dsc) [2044 B] Get:2 http://debian.oregonstate.edu/debian unstable/main stacks 2.53+dfsg-1 (tar) [321 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main stacks 2.53+dfsg-1 (diff) [7560 B] Fetched 331 kB in 0s (18.5 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/stacks-ZLtHDw/stacks-2.53+dfsg' with '<>' I: NOTICE: Log filtering will replace 'build/stacks-ZLtHDw' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 12), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [430 B] Get:5 copy:/<>/apt_archive ./ Packages [521 B] Fetched 1908 B in 0s (168 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbam-dev:armel libbrotli1:armel libbsd0 libbz2-1.0:armel libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libcurl3-gnutls:armel libdb5.3:armel libdebhelper-perl libdebian-dpkgcross-perl libdeflate0:armel libelf1 libffi7:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgcrypt20:armel libglib2.0-0 libgmp10:armel libgnutls30:armel libgomp1:armel libgomp1-armel-cross libgpg-error0:armel libgssapi-krb5-2:armel libhogweed5:armel libhts-dev:armel libhts3:armel libicu63 libidn2-0:armel libio-string-perl libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel libldap-2.4-2:armel libldap-common liblocale-gettext-perl liblzma-dev:armel liblzma5:armel libmagic-mgc libmagic1 libncurses6:armel libnettle7:armel libnghttp2-14:armel libp11-kit0:armel libpipeline1 libpsl5:armel librtmp1:armel libsasl2-2:armel libsasl2-modules-db:armel libsigsegv2 libsparsehash-dev libssh2-1:armel libssl1.1:armel libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtasn1-6:armel libtinfo6:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libunistring2:armel libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db po-debconf samtools:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armel libc-l10n:armel locales:armel glibc-doc manpages-dev:armel rng-tools:armel gnutls-bin:armel krb5-doc:armel krb5-user:armel liblzma-doc:armel libstdc++-9-doc libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx ca-certificates:armel libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libgpg-error-l10n:armel krb5-locales:armel libgpm2:armel publicsuffix:armel libsasl2-modules:armel libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl python3:armel cwltool:armel The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbam-dev:armel libbrotli1:armel libbsd0 libbz2-1.0:armel libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libcom-err2:armel libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libcurl3-gnutls:armel libdb5.3:armel libdebhelper-perl libdebian-dpkgcross-perl libdeflate0:armel libelf1 libffi7:armel libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libgcrypt20:armel libglib2.0-0 libgmp10:armel libgnutls30:armel libgomp1:armel libgomp1-armel-cross libgpg-error0:armel libgssapi-krb5-2:armel libhogweed5:armel libhts-dev:armel libhts3:armel libicu63 libidn2-0:armel libio-string-perl libk5crypto3:armel libkeyutils1:armel libkrb5-3:armel libkrb5support0:armel libldap-2.4-2:armel libldap-common liblocale-gettext-perl liblzma-dev:armel liblzma5:armel libmagic-mgc libmagic1 libncurses6:armel libnettle7:armel libnghttp2-14:armel libp11-kit0:armel libpipeline1 libpsl5:armel librtmp1:armel libsasl2-2:armel libsasl2-modules-db:armel libsigsegv2 libsparsehash-dev libssh2-1:armel libssl1.1:armel libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtasn1-6:armel libtinfo6:armel libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libunistring2:armel libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db po-debconf samtools:armel sbuild-build-depends-main-dummy:armel sensible-utils ucf zlib1g:armel zlib1g-dev:armel 0 upgraded, 136 newly installed, 0 to remove and 0 not upgraded. Need to get 91.4 MB of archives. After this operation, 342 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-5 [920 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.1-1 [1308 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main armel gcc-10-base armel 10-20200502-1 [197 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.3.0-11 [196 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.2-1 [775 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.34-6 [2749 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.16-1 [104 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.30-7 [2634 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.3.0-11 [1701 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.3.0-11 [10.7 MB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.3.0-8cross1 [197 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.3.0-8cross1 [6816 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.3.0-8cross1 [192 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10-20200418-1cross1 [192 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.30-2cross1 [1128 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 10-20200418-1cross1 [38.3 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 10-20200418-1cross1 [84.1 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 10-20200418-1cross1 [8812 B] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.3.0-8cross1 [340 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 10-20200418-1cross1 [368 kB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 10-20200418-1cross1 [114 kB] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.3.0-8cross1 [644 kB] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.3.0-8cross1 [7174 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.4.19-1cross1 [1155 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.30-2cross1 [2148 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.3.0-8cross1 [1712 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.3.0-8cross1 [7401 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000002-1 [52.0 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-3 [8296 kB] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.10+dfsg-5 [709 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-2 [343 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-14 [513 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 13 [184 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.8.0-1 [14.8 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.64.2-1 [1343 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 13 [1002 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 10-20200502-1 [38.2 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.16-1 [101 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.30-7 [2349 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.3.0-11 [347 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 10-20200502-1 [9008 B] Get:87 http://debian.oregonstate.edu/debian unstable/main armel libbam-dev armel 0.1.19-4 [112 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main armel libbrotli1 armel 1.0.7-6.1 [259 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main armel libbz2-1.0 armel 1.0.8-2 [45.3 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.6.7-1 [1080 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.16-1 [120 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.30-7 [2189 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main armel libcom-err2 armel 1.45.6-1 [71.0 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main armel libgmp10 armel 2:6.2.0+dfsg-4 [198 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main armel libnettle7 armel 3.5.1+really3.5.1-2 [232 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main armel libhogweed5 armel 3.5.1+really3.5.1-2 [127 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armel libunistring2 armel 0.9.10-2 [364 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armel libidn2-0 armel 2.3.0-1 [83.5 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armel libffi7 armel 3.3-4 [19.7 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armel libp11-kit0 armel 0.23.20-1 [310 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main armel libtasn1-6 armel 4.16.0-2 [49.8 kB] Get:102 http://debian.oregonstate.edu/debian unstable/main armel libgnutls30 armel 3.6.13-2 [1155 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armel libkrb5support0 armel 1.17-7 [61.4 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main armel libk5crypto3 armel 1.17-7 [112 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armel libkeyutils1 armel 1.6.1-2 [14.5 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armel libssl1.1 armel 1.1.1g-1 [1278 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armel libkrb5-3 armel 1.17-7 [320 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armel libgssapi-krb5-2 armel 1.17-7 [135 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armel libdb5.3 armel 5.3.28+dfsg1-0.6 [572 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main armel libsasl2-modules-db armel 2.1.27+dfsg-2 [67.6 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main armel libsasl2-2 armel 2.1.27+dfsg-2 [98.7 kB] Get:112 http://debian.oregonstate.edu/debian unstable/main amd64 libldap-common all 2.4.50+dfsg-1 [92.9 kB] Get:113 http://debian.oregonstate.edu/debian unstable/main armel libldap-2.4-2 armel 2.4.50+dfsg-1 [204 kB] Get:114 http://debian.oregonstate.edu/debian unstable/main armel libnghttp2-14 armel 1.40.0-1 [74.0 kB] Get:115 http://debian.oregonstate.edu/debian unstable/main armel libpsl5 armel 0.21.0-1 [53.9 kB] Get:116 http://debian.oregonstate.edu/debian unstable/main armel zlib1g armel 1:1.2.11.dfsg-2 [84.7 kB] Get:117 http://debian.oregonstate.edu/debian unstable/main armel librtmp1 armel 2.4+20151223.gitfa8646d.1-2+b1 [55.3 kB] Get:118 http://debian.oregonstate.edu/debian unstable/main armel libgpg-error0 armel 1.37-1 [63.1 kB] Get:119 http://debian.oregonstate.edu/debian unstable/main armel libgcrypt20 armel 1.8.5-5 [485 kB] Get:120 http://debian.oregonstate.edu/debian unstable/main armel libssh2-1 armel 1.8.0-2.1 [126 kB] Get:121 http://debian.oregonstate.edu/debian unstable/main armel libcurl3-gnutls armel 7.68.0-1 [284 kB] Get:122 http://debian.oregonstate.edu/debian unstable/main armel libdeflate0 armel 1.5-3 [43.5 kB] Get:123 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 10-20200502-1 [86.2 kB] Get:124 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 10-20200502-1 [409 kB] Get:125 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 10-20200502-1 [115 kB] Get:126 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.3.0-11 [647 kB] Get:127 http://debian.oregonstate.edu/debian unstable/main armel liblzma5 armel 5.2.4-1+b1 [144 kB] Get:128 http://debian.oregonstate.edu/debian unstable/main armel libhts3 armel 1.10.2-3 [323 kB] Get:129 http://debian.oregonstate.edu/debian unstable/main armel liblzma-dev armel 5.2.4-1+b1 [204 kB] Get:130 http://debian.oregonstate.edu/debian unstable/main armel zlib1g-dev armel 1:1.2.11.dfsg-2 [185 kB] Get:131 http://debian.oregonstate.edu/debian unstable/main armel libhts-dev armel 1.10.2-3 [4794 kB] Get:132 http://debian.oregonstate.edu/debian unstable/main armel libtinfo6 armel 6.2-1 [321 kB] Get:133 http://debian.oregonstate.edu/debian unstable/main armel libncurses6 armel 6.2-1 [81.5 kB] Get:134 http://debian.oregonstate.edu/debian unstable/main amd64 libsparsehash-dev all 2.0.3-2 [76.8 kB] Get:135 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.3.0-11 [1744 kB] Get:136 http://debian.oregonstate.edu/debian unstable/main armel samtools armel 1.10-3 [489 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 91.4 MB in 1s (113 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12639 files and directories currently installed.) Preparing to unpack .../000-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../001-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../002-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../003-groff-base_1.22.4-5_amd64.deb ... Unpacking groff-base (1.22.4-5) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../004-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../005-man-db_2.9.1-1_amd64.deb ... Unpacking man-db (2.9.1-1) ... 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Unpacking libmagic1:amd64 (1:5.38-4) ... Selecting previously unselected package file. Preparing to unpack .../012-file_1%3a5.38-4_amd64.deb ... Unpacking file (1:5.38-4) ... Selecting previously unselected package gettext-base. Preparing to unpack .../013-gettext-base_0.19.8.1-10_amd64.deb ... Unpacking gettext-base (0.19.8.1-10) ... Selecting previously unselected package ucf. Preparing to unpack .../014-ucf_3.0038+nmu1_all.deb ... Moving old data out of the way Unpacking ucf (3.0038+nmu1) ... Selecting previously unselected package libsigsegv2:amd64. Preparing to unpack .../015-libsigsegv2_2.12-2_amd64.deb ... Unpacking libsigsegv2:amd64 (2.12-2) ... Selecting previously unselected package m4. Preparing to unpack .../016-m4_1.4.18-4_amd64.deb ... Unpacking m4 (1.4.18-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../017-autoconf_2.69-11.1_all.deb ... Unpacking autoconf (2.69-11.1) ... Selecting previously unselected package autotools-dev. 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Selecting previously unselected package libubsan1-armel-cross. Preparing to unpack .../040-libubsan1-armel-cross_10-20200418-1cross1_all.deb ... Unpacking libubsan1-armel-cross (10-20200418-1cross1) ... Selecting previously unselected package libgcc-9-dev-armel-cross. Preparing to unpack .../041-libgcc-9-dev-armel-cross_9.3.0-8cross1_all.deb ... Unpacking libgcc-9-dev-armel-cross (9.3.0-8cross1) ... Selecting previously unselected package gcc-9-arm-linux-gnueabi. Preparing to unpack .../042-gcc-9-arm-linux-gnueabi_9.3.0-8cross1_amd64.deb ... Unpacking gcc-9-arm-linux-gnueabi (9.3.0-8cross1) ... Selecting previously unselected package gcc-arm-linux-gnueabi. Preparing to unpack .../043-gcc-arm-linux-gnueabi_4%3a9.2.1-3.1_amd64.deb ... Unpacking gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Selecting previously unselected package linux-libc-dev-armel-cross. Preparing to unpack .../044-linux-libc-dev-armel-cross_5.4.19-1cross1_all.deb ... Unpacking linux-libc-dev-armel-cross (5.4.19-1cross1) ... Selecting previously unselected package libc6-dev-armel-cross. Preparing to unpack .../045-libc6-dev-armel-cross_2.30-2cross1_all.deb ... Unpacking libc6-dev-armel-cross (2.30-2cross1) ... Selecting previously unselected package libstdc++-9-dev-armel-cross. Preparing to unpack .../046-libstdc++-9-dev-armel-cross_9.3.0-8cross1_all.deb ... Unpacking libstdc++-9-dev-armel-cross (9.3.0-8cross1) ... Selecting previously unselected package g++-9-arm-linux-gnueabi. Preparing to unpack .../047-g++-9-arm-linux-gnueabi_9.3.0-8cross1_amd64.deb ... Unpacking g++-9-arm-linux-gnueabi (9.3.0-8cross1) ... Selecting previously unselected package g++-arm-linux-gnueabi. Preparing to unpack .../048-g++-arm-linux-gnueabi_4%3a9.2.1-3.1_amd64.deb ... Unpacking g++-arm-linux-gnueabi (4:9.2.1-3.1) ... Selecting previously unselected package libconfig-inifiles-perl. Preparing to unpack .../049-libconfig-inifiles-perl_3.000002-1_all.deb ... Unpacking libconfig-inifiles-perl (3.000002-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../050-libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libicu63:amd64. Preparing to unpack .../051-libicu63_63.2-3_amd64.deb ... Unpacking libicu63:amd64 (63.2-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../052-libxml2_2.9.10+dfsg-5_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-5) ... Selecting previously unselected package libxml-namespacesupport-perl. Preparing to unpack .../053-libxml-namespacesupport-perl_1.12-1_all.deb ... Unpacking libxml-namespacesupport-perl (1.12-1) ... Selecting previously unselected package libxml-sax-base-perl. Preparing to unpack .../054-libxml-sax-base-perl_1.09-1_all.deb ... Unpacking libxml-sax-base-perl (1.09-1) ... Selecting previously unselected package libxml-sax-perl. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:amd64 (2.64.2-1) ... No schema files found: doing nothing. Setting up libdebhelper-perl (13) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up linux-libc-dev:armel (5.6.7-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libldap-common (2.4.50+dfsg-1) ... Setting up libyaml-perl (1.30-1) ... Setting up libsparsehash-dev (2.0.3-2) ... Setting up libicu63:amd64 (63.2-3) ... Setting up linux-libc-dev-armel-cross (5.4.19-1cross1) ... Setting up gcc-9-arm-linux-gnueabi-base:amd64 (9.3.0-8cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up gcc-10-base:armel (10-20200502-1) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up cpp-9-arm-linux-gnueabi (9.3.0-8cross1) ... Setting up autopoint (0.19.8.1-10) ... Setting up libbam-dev:armel (0.1.19-4) ... Setting up gcc-9-cross-base (9.3.0-8cross1) ... Setting up gcc-10-cross-base (10-20200418-1cross1) ... Setting up libc6-armel-cross (2.30-2cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.16-1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libc6-dev:amd64 (2.30-7) ... Setting up libc6-dev-armel-cross (2.30-2cross1) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-5) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:armel (9.3.0-11) ... Setting up libfile-stripnondeterminism-perl (1.8.0-1) ... Setting up libgomp1-armel-cross (10-20200418-1cross1) ... Setting up libstdc++-9-dev:amd64 (9.3.0-11) ... Setting up libtool (2.4.6-14) ... Setting up libgcc-s1-armel-cross (10-20200418-1cross1) ... Setting up m4 (1.4.18-4) ... Setting up libstdc++6-armel-cross (10-20200418-1cross1) ... Setting up libatomic1-armel-cross (10-20200418-1cross1) ... Setting up libasan5-armel-cross (9.3.0-8cross1) ... Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libubsan1-armel-cross (10-20200418-1cross1) ... Setting up bsdmainutils (11.1.2+b1) ... 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 libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up g++-9 (9.3.0-11) ... Setting up libgcc-9-dev-armel-cross (9.3.0-8cross1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.8.0-1) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-5) ... Setting up build-essential (12.8) ... Setting up automake (1:1.16.2-1) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up gettext (0.19.8.1-10) ... Setting up libstdc++-9-dev-armel-cross (9.3.0-8cross1) ... Setting up gcc-9-arm-linux-gnueabi (9.3.0-8cross1) ... Setting up man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up g++-9-arm-linux-gnueabi (9.3.0-8cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-libxml-perl (2.0134+dfsg-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up po-debconf (1.0.21) ... Setting up g++-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armel (12.8) ... Setting up libcrypt1:armel (1:4.4.16-1) ... Setting up libgcc-s1:armel (10-20200502-1) ... Setting up dh-autoreconf (19) ... Setting up libc6:armel (2.30-7) ... Setting up libnettle7:armel (3.5.1+really3.5.1-2) ... Setting up libcrypt-dev:armel (1:4.4.16-1) ... Setting up libtasn1-6:armel (4.16.0-2) ... Setting up libc6-dev:armel (2.30-7) ... Setting up libbz2-1.0:armel (1.0.8-2) ... Setting up libdb5.3:armel (5.3.28+dfsg1-0.6) ... Setting up libstdc++6:armel (10-20200502-1) ... Setting up libtinfo6:armel (6.2-1) ... Setting up libkeyutils1:armel (1.6.1-2) ... Setting up liblzma5:armel (5.2.4-1+b1) ... Setting up libgpg-error0:armel (1.37-1) ... Setting up libssl1.1:armel (1.1.1g-1) ... Setting up libbrotli1:armel (1.0.7-6.1) ... Setting up libffi7:armel (3.3-4) ... Setting up libnghttp2-14:armel (1.40.0-1) ... Setting up libunistring2:armel (0.9.10-2) ... Setting up libdeflate0:armel (1.5-3) ... Setting up libgcrypt20:armel (1.8.5-5) ... Setting up debhelper (13) ... Setting up zlib1g:armel (1:1.2.11.dfsg-2) ... Setting up libidn2-0:armel (2.3.0-1) ... Setting up libcom-err2:armel (1.45.6-1) ... Setting up libgomp1:armel (10-20200502-1) ... Setting up libkrb5support0:armel (1.17-7) ... Setting up libsasl2-modules-db:armel (2.1.27+dfsg-2) ... Setting up libasan5:armel (9.3.0-11) ... Setting up libgmp10:armel (2:6.2.0+dfsg-4) ... Setting up libncurses6:armel (6.2-1) ... Setting up libp11-kit0:armel (0.23.20-1) ... Setting up libatomic1:armel (10-20200502-1) ... Setting up libk5crypto3:armel (1.17-7) ... Setting up libsasl2-2:armel (2.1.27+dfsg-2) ... Setting up liblzma-dev:armel (5.2.4-1+b1) ... Setting up libubsan1:armel (10-20200502-1) ... Setting up zlib1g-dev:armel (1:1.2.11.dfsg-2) ... Setting up libssh2-1:armel (1.8.0-2.1) ... Setting up libkrb5-3:armel (1.17-7) ... Setting up libpsl5:armel (0.21.0-1) ... Setting up libhogweed5:armel (3.5.1+really3.5.1-2) ... Setting up libgcc-9-dev:armel (9.3.0-11) ... Setting up libgnutls30:armel (3.6.13-2) ... Setting up librtmp1:armel (2.4+20151223.gitfa8646d.1-2+b1) ... Setting up libgssapi-krb5-2:armel (1.17-7) ... Setting up libstdc++-9-dev:armel (9.3.0-11) ... Setting up libldap-2.4-2:armel (2.4.50+dfsg-1) ... Setting up libcurl3-gnutls:armel (7.68.0-1) ... Setting up libhts3:armel (1.10.2-3) ... Setting up libhts-dev:armel (1.10.2-3) ... Setting up samtools:armel (1.10-3) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.30-7) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-6 dpkg-dev_1.19.7 g++-9_9.3.0-11 gcc-9_9.3.0-11 libc6-dev_2.30-7 libstdc++-9-dev_9.3.0-11 libstdc++-9-dev-armel-cross_9.3.0-8cross1 libstdc++6_10-20200502-1 libstdc++6-armel-cross_10-20200418-1cross1 linux-libc-dev_5.6.7-1 Package versions: adduser_3.118 apt_2.1.0 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-6 binutils-arm-linux-gnueabi_2.34-6 binutils-common_2.34-6 binutils-x86-64-linux-gnu_2.34-6 bsdmainutils_11.1.2+b1 bsdutils_1:2.35.1-2 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.4.0-3 cpp-9_9.3.0-11 cpp-9-arm-linux-gnueabi_9.3.0-8cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-cross_2.6.15-3 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-2 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.3.0-11 g++-9-arm-linux-gnueabi_9.3.0-8cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10-20200502-1 gcc-10-cross-base_10-20200418-1cross1 gcc-8-base_8.4.0-3 gcc-9_9.3.0-11 gcc-9-arm-linux-gnueabi_9.3.0-8cross1 gcc-9-arm-linux-gnueabi-base_9.3.0-8cross1 gcc-9-base_9.3.0-11 gcc-9-cross-base_9.3.0-8cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg5.0_1.8.4 libapt-pkg6.0_2.1.0 libarchive-zip-perl_1.68-1 libasan5_9.3.0-11 libasan5-armel-cross_9.3.0-8cross1 libatomic1_10-20200502-1 libatomic1-armel-cross_10-20200418-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3+b1 libbam-dev_0.1.19-4 libbinutils_2.34-6 libblkid1_2.35.1-2 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-7 libc-dev-bin_2.30-7 libc6_2.30-7 libc6-armel-cross_2.30-2cross1 libc6-dev_2.30-7 libc6-dev-armel-cross_2.30-2cross1 libcap-ng0_0.7.9-2.1+b2 libcc1-0_10-20200502-1 libcom-err2_1.45.6-1 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000002-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-6 libctf0_2.34-6 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdebian-dpkgcross-perl_2.6.15-3 libdeflate0_1.5-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.1-2 libffi6_3.2.1-9 libffi7_3.3-4 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.8.0-1 libfile-which-perl_1.23-1 libgcc-9-dev_9.3.0-11 libgcc-9-dev-armel-cross_9.3.0-8cross1 libgcc-s1_10-20200502-1 libgcc-s1-armel-cross_10-20200418-1cross1 libgcc1_1:10-20200502-1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200502-1 libgomp1-armel-cross_10-20200418-1cross1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-3 libidn2-0_2.3.0-1 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22.1-1 libitm1_10-20200502-1 libk5crypto3_1.17-7 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7 libkrb5support0_1.17-7 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblsan0_10-20200502-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1+b1 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.35.1-2 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libmpx2_8.4.0-3 libncurses6_6.2-1 libncursesw6_6.2-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpsl5_0.21.0-1 libquadmath0_10-20200502-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+b1 libselinux1_3.0-1+b3 libsemanage-common_3.0-1 libsemanage1_3.0-1+b3 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-2 libsparsehash-dev_2.0.3-2 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-11 libstdc++-9-dev-armel-cross_9.3.0-8cross1 libstdc++6_10-20200502-1 libstdc++6-armel-cross_10-20200418-1cross1 libsub-override-perl_0.09-2 libsystemd0_245.5-2 libtasn1-6_4.16.0-2 libtinfo6_6.2-1 libtool_2.4.6-14 libtsan0_10-20200502-1 libubsan1_10-20200502-1 libubsan1-armel-cross_10-20200418-1cross1 libuchardet0_0.0.6-3 libudev1_245.5-2 libunistring2_0.9.10-2 libuuid1_2.35.1-2 libxml-libxml-perl_2.0134+dfsg-2 libxml-namespacesupport-perl_1.12-1 libxml-sax-base-perl_1.09-1 libxml-sax-perl_1.02+dfsg-1 libxml-simple-perl_2.25-1 libxml2_2.9.10+dfsg-5 libyaml-perl_1.30-1 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.6.7-1 linux-libc-dev-armel-cross_5.4.19-1cross1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.35.1-2 ncurses-base_6.2-1 ncurses-bin_6.2-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-10 po-debconf_1.0.21 samtools_1.10-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 ucf_3.0038+nmu1 util-linux_2.35.1-2 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: stacks Binary: stacks Architecture: any Version: 2.53+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Tim Booth , Andreas Tille Homepage: https://creskolab.uoregon.edu/stacks/ Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/stacks Vcs-Git: https://salsa.debian.org/med-team/stacks.git Build-Depends: debhelper-compat (= 12), zlib1g-dev, libbam-dev, libsparsehash-dev, samtools, libhts-dev Package-List: stacks deb science optional arch=any Checksums-Sha1: 9076f8acb14a8b62250a6690ec74286732748d27 321268 stacks_2.53+dfsg.orig.tar.xz 76b59db811a3f5099ba1d065f8efe419987cb373 7560 stacks_2.53+dfsg-1.debian.tar.xz Checksums-Sha256: 9e096890618b1d476f371dd92d03b0a09c8c07f696a878826e90487de50bb879 321268 stacks_2.53+dfsg.orig.tar.xz 51c060cd03b636405ac6601a6dc9aaef3205c9b67e104519b08d3f653b730e0f 7560 stacks_2.53+dfsg-1.debian.tar.xz Files: 5f930438163d8a79265e1b3acedb7b4f 321268 stacks_2.53+dfsg.orig.tar.xz 6c72e97fe3e76ceac4893aecb3b60221 7560 stacks_2.53+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl6kzvsTHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0ZzOD/4p+ckLtzcZIWgQHewzHbm1urAazXxt qffd0dFSnVJiURR/37D4fDPzKBWpVNwHFBjEG8lUshbnBDGAaPAF7g4LEkYRF1p0 xPQWsTYPe93ze+t4r/iDkGugffwIMzaNZ6nBxzuLqX+b0ZNVbk7+hw0MZaudQuSw c1BWTtdZYZybP3BUYJ9RDuzZ8etu+tpGQmnUslnD2q/NWR4g9ebsURBZ1Zreqif4 9FzzRBxPsadxKsbWmso2oVsHQniCAzgVZFLtgmaTuygx0FYiVFUPTxZnMSbs+kZ4 0AVh61c1YOpfwrpXhP/NlHPJzSc4PGK3G91DVM0LPBKWdVYCykMfSkixd8G3c31M pzq0eu/DB6F17NtXlQBlUI+7YmUbiDGsH1s6iymv2FhaWi4tbIA1mC5P6FEus92y knVskbH744+TR8T8qYgLWgAtlgaEpZ71P9K5dNvxpQmU1+gF7SA6WwIO19vSeXW9 WN7G2DstCK5lOMh2ykq7Q3ap+bKWIGz+zMSEgoTsjl5glGWEm9cS79/CjGKnP0lR CFQhFZErHbo4HSLrT6D1NdpZ+KSlPyI4EZrJdH9UxKqribydjDP3MzcWT7zlWEa2 pW9gRiVOYZM+cYKzEpQ1zvhbyIrsAzW74DrEFchYp74qaayTTCC7qShnmUqolRkV KoPf0PTlqcPM7A== =NrhF -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sat Apr 25 23:59:55 2020 UTC gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1 gpgv: issuer "moeller@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./stacks_2.53+dfsg-1.dsc dpkg-source: info: extracting stacks in /<> dpkg-source: info: unpacking stacks_2.53+dfsg.orig.tar.xz dpkg-source: info: unpacking stacks_2.53+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying RisR.patch dpkg-source: info: applying script-exe-paths dpkg-source: info: applying use_debian_packaged_htslib.patch dpkg-source: info: applying 2to3.patch Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-97963314-486d-49a7-8fb1-a2cc8f817081 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package stacks dpkg-buildpackage: info: source version 2.53+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Steffen Moeller dpkg-architecture: warning: specified GNU system type arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel debian/rules clean dh clean debian/rules override_dh_clean make[1]: Entering directory '/<>' dh_clean rm -f ./constants.php make[1]: Leaving directory '/<>' debian/rules binary-arch dh binary-arch dh_update_autotools_config -a dh_autoreconf -a configure.ac:33: installing 'config/ar-lib' configure.ac:28: installing 'config/compile' configure.ac:7: installing 'config/install-sh' configure.ac:7: installing 'config/missing' Makefile.am: installing 'config/depcomp' parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/<>' dh_auto_configure -- --enable-sparsehash --enable-bam \ --with-bam-include-path=/usr/include/samtools \ --with-bam-lib-path=/usr/lib ./configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabi --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --host=arm-linux-gnueabi --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib configure: WARNING: unrecognized options: --disable-maintainer-mode, --enable-sparsehash, --enable-bam, --with-bam-include-path, --with-bam-lib-path configure: loading site script /etc/dpkg-cross/cross-config.armel checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for arm-linux-gnueabi-strip... arm-linux-gnueabi-strip checking for a thread-safe mkdir -p... /bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for arm-linux-gnueabi-g++... arm-linux-gnueabi-g++ checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... yes checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether arm-linux-gnueabi-g++ accepts -g... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of arm-linux-gnueabi-g++... none checking for arm-linux-gnueabi-gcc... arm-linux-gnueabi-gcc checking whether we are using the GNU C compiler... yes checking whether arm-linux-gnueabi-gcc accepts -g... yes checking for arm-linux-gnueabi-gcc option to accept ISO C89... none needed checking whether arm-linux-gnueabi-gcc understands -c and -o together... yes checking dependency style of arm-linux-gnueabi-gcc... none checking whether arm-linux-gnueabi-g++ supports C++11 features by default... yes checking for arm-linux-gnueabi-ranlib... arm-linux-gnueabi-ranlib checking for arm-linux-gnueabi-ar... arm-linux-gnueabi-ar checking the archiver (arm-linux-gnueabi-ar) interface... ar checking for omp_set_num_threads in -lgomp... yes checking for gzread in -lz... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking how to run the C preprocessor... arm-linux-gnueabi-gcc -E checking for grep that handles long lines and -e... /bin/grep checking for egrep... /bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for arm-linux-gnueabi-gcc option to support OpenMP... -fopenmp checking for stdbool.h that conforms to C99... yes checking for _Bool... yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking whether closedir returns void... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... (cached) yes checking for floor... no checking for memset... yes checking for pow... no checking for sqrt... no checking for clock_gettime... yes checking for functional regular expressions... configure: WARNING: Requires g++ 4.9.0 or greater. no checking for gawk... (cached) mawk checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: WARNING: unrecognized options: --disable-maintainer-mode, --enable-sparsehash, --enable-bam, --with-bam-include-path, --with-bam-lib-path make[1]: Leaving directory '/<>' dh_auto_build -a make -j1 make[1]: Entering directory '/<>' make all-recursive make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/ustacks.o src/ustacks.cc In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from src/constants.h:40, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/arm-linux-gnueabi/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 = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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 = {Aln}; _Tp = Aln; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Aln}; _Tp = Aln; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/set:60, from src/constants.h:43, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1879 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/arm-linux-gnueabi/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 = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int GappedAln::trace_local_alignment(const string&, const string&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int GappedAln::trace_global_alignment(const string&, const string&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/arm-linux-gnueabi/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 = Aln; _Compare = __gnu_cxx::__ops::_Iter_comp_val]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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 = Aln; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘_Z28search_for_gapped_remaindersRSt3mapIiP11MergedStackSt4lessIiESaISt4pairIKiS1_EEERS_IiP5StackS3_SaIS4_IS5_SB_EEERS_IiP3RemS3_SaIS4_IS5_SH_EEE._omp_fn.0’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘int merge_gapped_alns(std::map&, std::map&, std::map&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:61, from src/constants.h:44, from src/ustacks.h:24, from src/ustacks.cc:25: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In function ‘int dump_stack_graph(std::string, std::map&, std::map&, std::vector&, std::map >&, std::map >&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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, arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/aln_utils.o src/aln_utils.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/BamI.o src/BamI.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/catalog_utils.o src/catalog_utils.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cmb.o src/cmb.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/constants.o src/constants.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNANSeq.o src/DNANSeq.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq4.o src/DNASeq4.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/DNASeq.o src/DNASeq.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gzFasta.o src/gzFasta.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/input.o src/input.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/locus.o src/locus.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/log_utils.o src/log_utils.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/MetaPopInfo.o src/MetaPopInfo.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/models.o src/models.cc In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from src/constants.h:40, from src/models.h:24, from src/models.cc:30: /usr/arm-linux-gnueabi/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 = {MarukiLowModel::LikData}; _Tp = MarukiLowModel::LikData; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {MarukiLowModel::LikData}; _Tp = MarukiLowModel::LikData; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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)...); | ^~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mstack.o src/mstack.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mst.o src/mst.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/nucleotides.o src/nucleotides.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/renz.o src/renz.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Seq.o src/Seq.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sql_utilities.o src/sql_utilities.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/stacks.o src/stacks.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/utils.o src/utils.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Vcf.o src/Vcf.cc rm -f libcore.a arm-linux-gnueabi-ar cru libcore.a src/aln_utils.o src/BamI.o src/catalog_utils.o src/cmb.o src/constants.o src/DNANSeq.o src/DNASeq4.o src/DNASeq.o src/gzFasta.o src/input.o src/kmers.o src/locus.o src/log_utils.o src/MetaPopInfo.o src/models.o src/mstack.o src/mst.o src/nucleotides.o src/renz.o src/Seq.o src/sql_utilities.o src/stacks.o src/utils.o src/Vcf.o arm-linux-gnueabi-ar: `u' modifier ignored since `D' is the default (see `U') arm-linux-gnueabi-ranlib libcore.a arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o ustacks src/ustacks.o -lhts libcore.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/cstacks.o src/cstacks.cc In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from src/MetaPopInfo.h:5, from src/cstacks.cc:25: /usr/arm-linux-gnueabi/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 = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/MetaPopInfo.h:8, from src/cstacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/MetaPopInfo.h:8, from src/cstacks.cc:25: /usr/arm-linux-gnueabi/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 = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/MetaPopInfo.h:8, from src/cstacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int GappedAln::trace_local_alignment(const string&, const string&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int GappedAln::trace_global_alignment(const string&, const string&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o cstacks src/cstacks.o -lhts libcore.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/sstacks.o src/sstacks.cc In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from /usr/arm-linux-gnueabi/include/c++/9/regex:38, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1820 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1839 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from /usr/arm-linux-gnueabi/include/c++/9/regex:38, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Distance = int; _Tp = std::pair, AlignRes>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from /usr/arm-linux-gnueabi/include/c++/9/regex:51, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/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 = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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, std::allocator >, AlignRes>}; _Tp = std::pair, AlignRes>; _Alloc = std::allocator, AlignRes> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector, AlignRes> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’} changed in GCC 7.1 426 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:60, from /usr/arm-linux-gnueabi/include/c++/9/regex:52, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/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, AlignRes>; _KeyOfValue = std::_Select1st, AlignRes> >; _Compare = std::less >; _Alloc = std::allocator, AlignRes> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, AlignRes> >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from /usr/arm-linux-gnueabi/include/c++/9/regex:38, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from /usr/arm-linux-gnueabi/include/c++/9/regex:38, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/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 = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from /usr/arm-linux-gnueabi/include/c++/9/regex:38, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int GappedAln::trace_local_alignment(const string&, const string&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int GappedAln::trace_global_alignment(const string&, const string&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)::, AlignRes>&, std::pair, AlignRes>&)> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1939 | __introsort_loop(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from /usr/arm-linux-gnueabi/include/c++/9/regex:51, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In function ‘bool verify_gapped_match(std::map&, QLocus*, std::set&, std::map, std::map, AlignRes> >&, uint&, uint&, uint&, uint&, uint&)’: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ^~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from /usr/arm-linux-gnueabi/include/c++/9/regex:38, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1967 | std::__introsort_loop(__first, __last, | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 1968 | std::__lg(__last - __first) * 2, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1969 | __comp); | ~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator, AlignRes>*, std::vector, AlignRes> > >’ changed in GCC 7.1 1889 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:61, from /usr/arm-linux-gnueabi/include/c++/9/regex:52, from src/sstacks.cc:25: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In function ‘_Z15search_for_gapsRSt3mapIiP5LocusSt4lessIiESaISt4pairIKiS1_EEERS_IiP6QLocusS3_SaIS4_IS5_SB_EEERSt13unordered_mapIPKcSt6vectorIiSaIiEE12hash_charptr5eqstrSaIS4_IKSI_SL_EEERS_IiS4_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiES3_SaIS4_IS5_SZ_EEEd._omp_fn.0’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, AlignRes>, std::_Select1st, AlignRes> >, std::less >, std::allocator, AlignRes> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, AlignRes> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o sstacks src/sstacks.o -lhts libcore.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_radtags.o src/process_radtags.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clean.o src/clean.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/file_io.o src/file_io.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/write.o src/write.cc rm -f libclean.a arm-linux-gnueabi-ar cru libclean.a src/clean.o src/file_io.o src/write.o arm-linux-gnueabi-ar: `u' modifier ignored since `D' is the default (see `U') arm-linux-gnueabi-ranlib libclean.a arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_radtags src/process_radtags.o -lhts libcore.a libclean.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/process_shortreads.o src/process_shortreads.cc arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o process_shortreads src/process_shortreads.o -lhts libcore.a libclean.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmer_filter.o src/kmer_filter.cc arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o kmer_filter src/kmer_filter.o -lhts libcore.a libclean.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/clone_filter.o src/clone_filter.cc arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o clone_filter src/clone_filter.o -lhts libcore.a libclean.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/populations.o src/populations.cc In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from src/populations.h:40, from src/populations.cc:29: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/populations.h:44, from src/populations.cc:29: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1879 | __final_insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/populations.h:44, from src/populations.cc:29: /usr/arm-linux-gnueabi/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 = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/populations.h:44, from src/populations.cc:29: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘int bootstrap_fst_approximate_dist(std::vector&, std::vector&, double*, int*, std::map >&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In function ‘int bootstrap_popstats_approximate_dist(std::vector&, std::vector&, std::vector&, double*, int*, int, std::map >&, std::map >&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 1970 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/export_formats.o src/export_formats.cc src/export_formats.cc: In member function ‘virtual int PhylipVarAllExport::post_processing()’: src/export_formats.cc:2319:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘std::size_t’ {aka ‘unsigned int’} [-Wformat=] 2319 | sprintf(s, "%11lu", this->_seq_len); | ~~~~^ ~~~~~~~~~~~~~~ | | | | | std::size_t {aka unsigned int} | long unsigned int | %11u arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/mapping_utils.o src/mapping_utils.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/genotype_dictionaries.o src/genotype_dictionaries.cc arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/PopSum.o src/PopSum.cc In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from src/PopSum.h:26, from src/PopSum.cc:21: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/map:60, from src/PopSum.h:27, from src/PopSum.cc:21: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h: In member function ‘std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:2187:5: 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 2187 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/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 /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, double>; _KeyOfValue = std::_Select1st, double> >; _Compare = std::less >; _Alloc = std::allocator, double> >]’: /usr/arm-linux-gnueabi/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 In file included from /usr/arm-linux-gnueabi/include/c++/9/map:61, from src/PopSum.h:27, from src/PopSum.cc:21: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In function ‘double count_haplotypes_at_locus(int, int, const Datum* const*, std::map, double>&)’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:518:8: 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 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:518:8: 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 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In member function ‘LocStat* LocPopSum::haplotype_diversity(int, int, const Datum* const*)’: /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In member function ‘double LocusDivergence::haplotype_d_est(const Datum**, const LocSum**, std::vector&)’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:518:8: 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 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:518:8: 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 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:518:8: 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 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:518:8: 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 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In member function ‘double LocusDivergence::haplotype_dxy(const Datum**, std::size_t, std::vector&)’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:518:8: 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 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:518:8: 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 7.1 518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/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, /usr/arm-linux-gnueabi/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, arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/Hwp.o src/Hwp.cc src/Hwp.cc: In member function ‘void HWMatrix::dump_matrix()’: src/Hwp.cc:383:43: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 5 has type ‘std::size_t’ {aka ‘unsigned int’} [-Wformat=] 383 | snprintf(buf, id_len, "%*lu ", padding, this->_g[i][j]); | ~~~^ ~~~~~~~~~~~~~~ | | | | long unsigned int std::size_t {aka unsigned int} | %*u rm -f libpop.a arm-linux-gnueabi-ar cru libpop.a src/export_formats.o src/mapping_utils.o src/genotype_dictionaries.o src/PopSum.o src/Hwp.o arm-linux-gnueabi-ar: `u' modifier ignored since `D' is the default (see `U') arm-linux-gnueabi-ranlib libpop.a arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o populations src/populations.o -lhts libcore.a libpop.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/phasedstacks.o src/phasedstacks.cc In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from src/phasedstacks.h:39, from src/phasedstacks.cc:25: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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)...); | ^~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o phasedstacks src/phasedstacks.o -lhts libcore.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/tsv2bam.o src/tsv2bam.cc arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o tsv2bam src/tsv2bam.o -lhts libcore.a -lz -lgomp arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/gstacks.o src/gstacks.cc src/gstacks.cc: In member function ‘bool LocusProcessor::align_reads_to_contig(SuffixTree*, GappedAln*, DNASeq4&, AlignRes&) const’: src/gstacks.cc:1319:32: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::__cxx11::basic_string::size_type’ {aka ‘unsigned int’} [-Wformat=] 1319 | snprintf(c, id_len, "%luM", query.length()); | ~~^ ~~~~~~~~~~~~~~ | | | | | std::__cxx11::basic_string::size_type {aka unsigned int} | long unsigned int | %u src/gstacks.cc: In member function ‘std::size_t LocusProcessor::find_locus_overlap(SuffixTree*, GappedAln*, const DNASeq4&, std::string&) const’: src/gstacks.cc:1505:38: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘std::size_t’ {aka ‘unsigned int’} [-Wformat=] 1505 | snprintf(buf, id_len, "%luM", alns.front().aln_len); | ~~^ ~~~~~~~~~~~~~~~~~~~~ | | | | long unsigned int std::size_t {aka unsigned int} | %u In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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&, std::vector&) const:: >]’: /usr/arm-linux-gnueabi/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, | ^~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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 = STAln; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, std::vector&) const:: >]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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&, std::vector&) const:: >]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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&, std::vector&) const:: >]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from src/constants.h:40, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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 STAln&}; _Tp = STAln; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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 double&}; _Tp = double; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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 = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {AlignRes}; _Tp = AlignRes; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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 = {STAln}; _Tp = STAln; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {STAln}; _Tp = STAln; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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 = {STLink}; _Tp = STLink; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int LocusProcessor::suffix_tree_hits_to_dag(std::size_t, std::vector&, std::vector&) const’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/vector:72, from src/constants.h:40, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/vector:67, from src/constants.h:40, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/vector:72, from src/constants.h:40, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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>:: | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h:61, from /usr/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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 = AlignRes; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/algorithm:62, from src/constants.h:53, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int GappedAln::trace_local_alignment(const string&, const string&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /usr/arm-linux-gnueabi/include/c++/9/bits/stl_algo.h: In member function ‘int GappedAln::trace_global_alignment(const string&, const string&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/vector:72, from src/constants.h:40, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void LocusProcessor::write_one_locus(const CLocAlnSet&, const std::vector&, const std::vector&, const std::vector >&)’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/vector:67, from src/constants.h:40, from src/gstacks.h:23, from src/gstacks.cc:23: /usr/arm-linux-gnueabi/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); | ^~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/debruijn.o src/debruijn.cc In file included from /usr/arm-linux-gnueabi/include/c++/9/vector:72, from src/constants.h:40, from src/debruijn.cc:5: /usr/arm-linux-gnueabi/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 = {Node}; _Tp = Node; _Alloc = std::allocator]’: /usr/arm-linux-gnueabi/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/arm-linux-gnueabi/include/c++/9/bits/vector.tcc: In member function ‘void Graph::rebuild(const std::vector&, std::size_t)’: /usr/arm-linux-gnueabi/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)...); | ^~~~~~~~~~~~~~~~~ arm-linux-gnueabi-g++ -DHAVE_CONFIG_H -I. -fopenmp -I./htslib -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/SuffixTree.o src/SuffixTree.cc arm-linux-gnueabi-g++ -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -Wl,-z,relro -Wl,-z,now -o gstacks src/gstacks.o src/debruijn.o src/SuffixTree.o -lhts libcore.a -lz -lgomp make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' create-stamp debian/debhelper-build-stamp dh_testroot -a dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/<>' dh_auto_install --no-parallel make -j1 install DESTDIR=/<>/stacks-2.53\+dfsg/debian/stacks AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/<>' make[3]: Entering directory '/<>' make[4]: Entering directory '/<>' /bin/mkdir -p '/<>/debian/stacks/usr/bin' /usr/bin/install -c ustacks cstacks sstacks process_radtags process_shortreads kmer_filter clone_filter populations phasedstacks tsv2bam gstacks '/<>/debian/stacks/usr/bin' /bin/mkdir -p '/<>/debian/stacks/usr/bin' /usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/integrate_alignments.py scripts/count_fixed_catalog_snps.py scripts/stacks-integrate-alignments scripts/stacks-dist-extract scripts/stacks-gdb scripts/stacks-samtools-tview scripts/stacks-count-reads-per-sample-per-locus scripts/stacks-hist2d-loci-samples-coverage '/<>/debian/stacks/usr/bin' make install-data-hook make[5]: Entering directory '/<>' sed -e 's,_VERSION_,2.53,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<>/debian/stacks/usr/bin/denovo_map.pl > /<>/debian/stacks/usr/bin/denovo_map.pl.subst mv /<>/debian/stacks/usr/bin/denovo_map.pl.subst /<>/debian/stacks/usr/bin/denovo_map.pl chmod +x /<>/debian/stacks/usr/bin/denovo_map.pl sed -e 's,_VERSION_,2.53,' -e 's,_BINDIR_,/usr/lib/stacks/bin/,g' -e 's,_PKGDATADIR_,/usr/share/stacks/,g' /<>/debian/stacks/usr/bin/ref_map.pl > /<>/debian/stacks/usr/bin/ref_map.pl.subst mv /<>/debian/stacks/usr/bin/ref_map.pl.subst /<>/debian/stacks/usr/bin/ref_map.pl chmod +x /<>/debian/stacks/usr/bin/ref_map.pl sed -i.bkp -e 's,_VERSION_,2.53,' /<>/debian/stacks/usr/bin/stacks-integrate-alignments sed -i.bkp -e 's,_VERSION_,2.53,' /<>/debian/stacks/usr/bin/stacks-samtools-tview rm -f /<>/debian/stacks/usr/bin/stacks-integrate-alignments.bkp rm -f /<>/debian/stacks/usr/bin/stacks-samtools-tview.bkp chmod +x /<>/debian/stacks/usr/bin/stacks-integrate-alignments chmod +x /<>/debian/stacks/usr/bin/stacks-dist-extract chmod +x /<>/debian/stacks/usr/bin/stacks-gdb make[5]: Leaving directory '/<>' make[4]: Leaving directory '/<>' make[3]: Leaving directory '/<>' make[2]: Leaving directory '/<>' make[1]: Leaving directory '/<>' debian/rules override_dh_install make[1]: Entering directory '/<>' mkdir -p debian/stacks/usr/lib/stacks mv debian/stacks/usr/bin debian/stacks/usr/lib/stacks cd debian/stacks/usr/lib/stacks/bin && \ for f in *.pl ; do \ ln -s "$f" "`basename $f .pl`" ; \ sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' $f ; \ done dh_install make[1]: Leaving directory '/<>' dh_installdocs -a dh_installchangelogs -a dh_perl -a debian/rules override_dh_link make[1]: Entering directory '/<>' dh_link mkdir -p debian/stacks/usr/lib/debian-med/bin cd debian/stacks/usr/lib/debian-med/bin && \ for f in `ls /<>/debian/stacks/usr/lib/stacks/bin` ; do \ ln -s ../../stacks/bin/$f ; \ done make[1]: Leaving directory '/<>' dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/populations contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_shortreads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/gstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/clone_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/ustacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/phasedstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/cstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/kmer_filter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/tsv2bam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/process_radtags contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dpkg-shlibdeps: warning: debian/stacks/usr/lib/stacks/bin/sstacks contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin dh_installdeb -a dh_gencontrol -a dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dpkg-gencontrol: warning: package stacks: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'stacks' in '../stacks_2.53+dfsg-1_armel.deb'. dpkg-deb: building package 'stacks-dbgsym' in '../stacks-dbgsym_2.53+dfsg-1_armel.deb'. dpkg-genbuildinfo --build=any dpkg-genchanges --build=any >../stacks_2.53+dfsg-1_armel.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 2020-05-06T21:06:26Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes | +------------------------------------------------------------------------------+ stacks_2.53+dfsg-1_armel.changes: --------------------------------- Format: 1.8 Date: Sun, 26 Apr 2020 01:41:49 +0200 Source: stacks Binary: stacks stacks-dbgsym Built-For-Profiles: cross nocheck Architecture: armel Version: 2.53+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Steffen Moeller Description: stacks - pipeline for building loci from short-read DNA sequences Changes: stacks (2.53+dfsg-1) unstable; urgency=medium . * Team upload. * New upstream version * Updated bio.tools entry to lower-case * Added dependency on littler to allow execution of R script Checksums-Sha1: 3a04ba9ebebb26554b162dbb7e310a7a127ad10c 26825168 stacks-dbgsym_2.53+dfsg-1_armel.deb 8aefeff5ed97d11dcb55d46d3a0d9d257dd4dc20 5545 stacks_2.53+dfsg-1_armel.buildinfo b51b52428c1415a28fe396a86d66ef06bfa16a57 894032 stacks_2.53+dfsg-1_armel.deb Checksums-Sha256: 742fa3064d925077fd97e05de72e98d8c4fb2aede12e0a588797436eeb34010d 26825168 stacks-dbgsym_2.53+dfsg-1_armel.deb fadd774ff37bc0f3de6eb2f2bad61ce6c8231ae77a63dd9d19d96ada3b790770 5545 stacks_2.53+dfsg-1_armel.buildinfo 5335a91961563596b9a947f3504fa1ef9debfe06cc242cf48c4744922da370ec 894032 stacks_2.53+dfsg-1_armel.deb Files: 8e647a635ae0f71bfc7f02ed89bf07e1 26825168 debug optional stacks-dbgsym_2.53+dfsg-1_armel.deb 5d96a3591328ed5cd14426aead86e67c 5545 science optional stacks_2.53+dfsg-1_armel.buildinfo c77a07376261e19f835da1f947950b5f 894032 science optional stacks_2.53+dfsg-1_armel.deb +------------------------------------------------------------------------------+ | Buildinfo | +------------------------------------------------------------------------------+ Format: 1.0 Source: stacks Binary: stacks Architecture: armel Version: 2.53+dfsg-1 Checksums-Md5: 8e647a635ae0f71bfc7f02ed89bf07e1 26825168 stacks-dbgsym_2.53+dfsg-1_armel.deb c77a07376261e19f835da1f947950b5f 894032 stacks_2.53+dfsg-1_armel.deb Checksums-Sha1: 3a04ba9ebebb26554b162dbb7e310a7a127ad10c 26825168 stacks-dbgsym_2.53+dfsg-1_armel.deb b51b52428c1415a28fe396a86d66ef06bfa16a57 894032 stacks_2.53+dfsg-1_armel.deb Checksums-Sha256: 742fa3064d925077fd97e05de72e98d8c4fb2aede12e0a588797436eeb34010d 26825168 stacks-dbgsym_2.53+dfsg-1_armel.deb 5335a91961563596b9a947f3504fa1ef9debfe06cc242cf48c4744922da370ec 894032 stacks_2.53+dfsg-1_armel.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Wed, 06 May 2020 21:06:26 +0000 Build-Path: /<> Installed-Build-Depends: autoconf (= 2.69-11.1), automake (= 1:1.16.2-1), autopoint (= 0.19.8.1-10), autotools-dev (= 20180224.1), base-files (= 11), base-passwd (= 3.5.47), bash (= 5.0-6), binutils (= 2.34-6), binutils-common (= 2.34-6), binutils-x86-64-linux-gnu (= 2.34-6), bsdmainutils (= 11.1.2+b1), bsdutils (= 1:2.35.1-2), build-essential (= 12.8), bzip2 (= 1.0.8-2), coreutils (= 8.30-3+b1), cpp (= 4:9.2.1-3.1), cpp-9 (= 9.3.0-11), dash (= 0.5.10.2-7), debconf (= 1.5.74), debhelper (= 13), debianutils (= 4.9.1), dh-autoreconf (= 19), dh-strip-nondeterminism (= 1.8.0-1), diffutils (= 1:3.7-3), dpkg (= 1.19.7), dpkg-dev (= 1.19.7), dwz (= 0.13-5), file (= 1:5.38-4), findutils (= 4.7.0-1), g++ (= 4:9.2.1-3.1), g++-9 (= 9.3.0-11), gcc (= 4:9.2.1-3.1), gcc-10-base (= 10-20200502-1), gcc-9 (= 9.3.0-11), gcc-9-base (= 9.3.0-11), gettext (= 0.19.8.1-10), gettext-base (= 0.19.8.1-10), grep (= 3.4-1), groff-base (= 1.22.4-5), gzip (= 1.10-2), hostname (= 3.23), init-system-helpers (= 1.57), intltool-debian (= 0.35.0+20060710.5), libacl1 (= 2.2.53-8), libarchive-zip-perl (= 1.68-1), libasan5 (= 9.3.0-11), libatomic1 (= 10-20200502-1), libattr1 (= 1:2.4.48-5), libaudit-common (= 1:2.8.5-3), libaudit1 (= 1:2.8.5-3+b1), libbam-dev (= 0.1.19-4), libbinutils (= 2.34-6), libblkid1 (= 2.35.1-2), libbrotli1 (= 1.0.7-6.1), libbsd0 (= 0.10.0-1), libbz2-1.0 (= 1.0.8-2), libc-bin (= 2.30-7), libc-dev-bin (= 2.30-7), libc6 (= 2.30-7), libc6-dev (= 2.30-7), libcap-ng0 (= 0.7.9-2.1+b2), libcc1-0 (= 10-20200502-1), libcom-err2 (= 1.45.6-1), libcroco3 (= 0.6.13-1), libcrypt-dev (= 1:4.4.16-1), libcrypt1 (= 1:4.4.16-1), libctf-nobfd0 (= 2.34-6), libctf0 (= 2.34-6), libcurl3-gnutls (= 7.68.0-1), libdb5.3 (= 5.3.28+dfsg1-0.6), libdebconfclient0 (= 0.251), libdebhelper-perl (= 13), libdeflate0 (= 1.5-3), libdpkg-perl (= 1.19.7), libelf1 (= 0.176-1.1), libffi7 (= 3.3-4), libfile-stripnondeterminism-perl (= 1.8.0-1), libgcc-9-dev (= 9.3.0-11), libgcc-s1 (= 10-20200502-1), libgcc1 (= 1:10-20200502-1), libgcrypt20 (= 1.8.5-5), libgdbm-compat4 (= 1.18.1-5), libgdbm6 (= 1.18.1-5), libglib2.0-0 (= 2.64.2-1), libgmp10 (= 2:6.2.0+dfsg-4), libgnutls30 (= 3.6.13-2), libgomp1 (= 10-20200502-1), libgpg-error0 (= 1.37-1), libgssapi-krb5-2 (= 1.17-7), libhogweed5 (= 3.5.1+really3.5.1-2), libhts-dev (= 1.10.2-3), libhts3 (= 1.10.2-3), libicu63 (= 63.2-3), libidn2-0 (= 2.3.0-1), libisl22 (= 0.22.1-1), libitm1 (= 10-20200502-1), libk5crypto3 (= 1.17-7), libkeyutils1 (= 1.6.1-2), libkrb5-3 (= 1.17-7), libkrb5support0 (= 1.17-7), libldap-2.4-2 (= 2.4.50+dfsg-1), libldap-common (= 2.4.50+dfsg-1), liblsan0 (= 10-20200502-1), liblz4-1 (= 1.9.2-2), liblzma-dev (= 5.2.4-1+b1), liblzma5 (= 5.2.4-1+b1), libmagic-mgc (= 1:5.38-4), libmagic1 (= 1:5.38-4), libmount1 (= 2.35.1-2), libmpc3 (= 1.1.0-1), libmpfr6 (= 4.0.2-1), libncurses6 (= 6.2-1), libnettle7 (= 3.5.1+really3.5.1-2), libnghttp2-14 (= 1.40.0-1), libp11-kit0 (= 0.23.20-1), libpam-modules (= 1.3.1-5), libpam-modules-bin (= 1.3.1-5), libpam-runtime (= 1.3.1-5), libpam0g (= 1.3.1-5), libpcre2-8-0 (= 10.34-7), libpcre3 (= 2:8.39-12+b1), libperl5.30 (= 5.30.0-10), libpipeline1 (= 1.5.2-2), libpsl5 (= 0.21.0-1), libquadmath0 (= 10-20200502-1), librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b1), libsasl2-2 (= 2.1.27+dfsg-2), libsasl2-modules-db (= 2.1.27+dfsg-2), libseccomp2 (= 2.4.3-1+b1), libselinux1 (= 3.0-1+b3), libsigsegv2 (= 2.12-2), libsmartcols1 (= 2.35.1-2), libsparsehash-dev (= 2.0.3-2), libssh2-1 (= 1.8.0-2.1), libssl1.1 (= 1.1.1g-1), libstdc++-9-dev (= 9.3.0-11), libstdc++6 (= 10-20200502-1), libsub-override-perl (= 0.09-2), libsystemd0 (= 245.5-2), libtasn1-6 (= 4.16.0-2), libtinfo6 (= 6.2-1), libtool (= 2.4.6-14), libtsan0 (= 10-20200502-1), libubsan1 (= 10-20200502-1), libuchardet0 (= 0.0.6-3), libudev1 (= 245.5-2), libunistring2 (= 0.9.10-2), libuuid1 (= 2.35.1-2), libxml2 (= 2.9.10+dfsg-5), linux-libc-dev (= 5.6.7-1), login (= 1:4.8.1-1), lsb-base (= 11.1.0), m4 (= 1.4.18-4), make (= 4.2.1-2), man-db (= 2.9.1-1), mawk (= 1.3.4.20200120-2), ncurses-base (= 6.2-1), ncurses-bin (= 6.2-1), patch (= 2.7.6-6), perl (= 5.30.0-10), perl-base (= 5.30.0-10), perl-modules-5.30 (= 5.30.0-10), po-debconf (= 1.0.21), samtools (= 1.10-3), sed (= 4.7-1), sensible-utils (= 0.0.12+nmu1), sysvinit-utils (= 2.96-3), tar (= 1.30+dfsg-7), util-linux (= 2.35.1-2), xz-utils (= 5.2.4-1+b1), zlib1g (= 1:1.2.11.dfsg-2), zlib1g-dev (= 1:1.2.11.dfsg-2) Environment: DEB_BUILD_OPTIONS="nocheck parallel=1" DEB_BUILD_PROFILES="cross nocheck" LANG="en_US.UTF-8" LC_ALL="C.UTF-8" SOURCE_DATE_EPOCH="1587858109" +------------------------------------------------------------------------------+ | Package contents | +------------------------------------------------------------------------------+ stacks-dbgsym_2.53+dfsg-1_armel.deb ----------------------------------- new Debian package, version 2.0. size 26825168 bytes: control archive=1092 bytes. 786 bytes, 12 lines control 1250 bytes, 12 lines md5sums Package: stacks-dbgsym Source: stacks Version: 2.53+dfsg-1 Auto-Built-Package: debug-symbols Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 27681 Depends: stacks (= 2.53+dfsg-1) Section: debug Priority: optional Description: debug symbols for stacks Build-Ids: 0ec0796a311dbe13e64b4ae7dddab9e84c01e1f3 15ad1f2643816cc2fa2e60c436d792ff2fbcfe39 2bfe882c853e3add4e9f3551c3fb1cca40370b82 391e3ff7feadb3a77e623f87fffbf53a553c6678 5a43d70ce9a31c18b0c41cb46678bcf5bca79ea0 75f67899ef6de68af6c2590cef7293beaa90700b 77b7ccea1ee1007b0a6b325c0adf71a121255c02 b35585cb368411db3503ed34b9a91f8dedf19fcd e59139a625ff45b8b800ee4bf84f97a0e98fa994 f8a58c06759bfb2d9af96267c3afc01c784f3c3c fe6a7bb71a09efae9e8498bfd00e82ccc371f0c3 drwxr-xr-x root/root 0 2020-04-25 23:41 ./ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/0e/ -rw-r--r-- root/root 1090460 2020-04-25 23:41 ./usr/lib/debug/.build-id/0e/c0796a311dbe13e64b4ae7dddab9e84c01e1f3.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/15/ -rw-r--r-- root/root 2035440 2020-04-25 23:41 ./usr/lib/debug/.build-id/15/ad1f2643816cc2fa2e60c436d792ff2fbcfe39.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/2b/ -rw-r--r-- root/root 5091916 2020-04-25 23:41 ./usr/lib/debug/.build-id/2b/fe882c853e3add4e9f3551c3fb1cca40370b82.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/39/ -rw-r--r-- root/root 2110576 2020-04-25 23:41 ./usr/lib/debug/.build-id/39/1e3ff7feadb3a77e623f87fffbf53a553c6678.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/5a/ -rw-r--r-- root/root 2046780 2020-04-25 23:41 ./usr/lib/debug/.build-id/5a/43d70ce9a31c18b0c41cb46678bcf5bca79ea0.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/75/ -rw-r--r-- root/root 1994412 2020-04-25 23:41 ./usr/lib/debug/.build-id/75/f67899ef6de68af6c2590cef7293beaa90700b.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/77/ -rw-r--r-- root/root 2291552 2020-04-25 23:41 ./usr/lib/debug/.build-id/77/b7ccea1ee1007b0a6b325c0adf71a121255c02.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/b3/ -rw-r--r-- root/root 1453668 2020-04-25 23:41 ./usr/lib/debug/.build-id/b3/5585cb368411db3503ed34b9a91f8dedf19fcd.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/e5/ -rw-r--r-- root/root 4442336 2020-04-25 23:41 ./usr/lib/debug/.build-id/e5/9139a625ff45b8b800ee4bf84f97a0e98fa994.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/f8/ -rw-r--r-- root/root 1744592 2020-04-25 23:41 ./usr/lib/debug/.build-id/f8/a58c06759bfb2d9af96267c3afc01c784f3c3c.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.build-id/fe/ -rw-r--r-- root/root 2808088 2020-04-25 23:41 ./usr/lib/debug/.build-id/fe/6a7bb71a09efae9e8498bfd00e82ccc371f0c3.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.dwz/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debug/.dwz/arm-linux-gnueabi/ -rw-r--r-- root/root 1207656 2020-04-25 23:41 ./usr/lib/debug/.dwz/arm-linux-gnueabi/stacks.debug drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/share/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/share/doc/ lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/share/doc/stacks-dbgsym -> stacks stacks_2.53+dfsg-1_armel.deb ---------------------------- new Debian package, version 2.0. size 894032 bytes: control archive=1628 bytes. 1002 bytes, 21 lines control 1798 bytes, 26 lines md5sums Package: stacks Version: 2.53+dfsg-1 Architecture: armel Maintainer: Debian Med Packaging Team Installed-Size: 4613 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libhts3 (>= 1.10), libstdc++6 (>= 9), zlib1g (>= 1:1.2.6), samtools, libdbi-perl Recommends: libspreadsheet-writeexcel-perl, python3, littler Conflicts: stacks-web Replaces: stacks-web Provides: stacks-web Section: science Priority: optional Homepage: https://creskolab.uoregon.edu/stacks/ Description: pipeline for building loci from short-read DNA sequences Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. . Note that this package installs Stacks such that all commands must be run as: $ stacks drwxr-xr-x root/root 0 2020-04-25 23:41 ./ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/bin/ -rwxr-xr-x root/root 771 2020-03-26 01:24 ./usr/bin/stacks drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/ lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/clone_filter -> ../../stacks/bin/clone_filter lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/count_fixed_catalog_snps.py -> ../../stacks/bin/count_fixed_catalog_snps.py lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/cstacks -> ../../stacks/bin/cstacks lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/denovo_map -> ../../stacks/bin/denovo_map lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/denovo_map.pl -> ../../stacks/bin/denovo_map.pl lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/gstacks -> ../../stacks/bin/gstacks lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/integrate_alignments.py -> ../../stacks/bin/integrate_alignments.py lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/kmer_filter -> ../../stacks/bin/kmer_filter lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/phasedstacks -> ../../stacks/bin/phasedstacks lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/populations -> ../../stacks/bin/populations lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/process_radtags -> ../../stacks/bin/process_radtags lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/process_shortreads -> ../../stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/ref_map -> ../../stacks/bin/ref_map lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/ref_map.pl -> ../../stacks/bin/ref_map.pl lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/sstacks -> ../../stacks/bin/sstacks lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/stacks-count-reads-per-sample-per-locus -> ../../stacks/bin/stacks-count-reads-per-sample-per-locus lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/stacks-dist-extract -> ../../stacks/bin/stacks-dist-extract lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/stacks-gdb -> ../../stacks/bin/stacks-gdb lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/stacks-hist2d-loci-samples-coverage -> ../../stacks/bin/stacks-hist2d-loci-samples-coverage lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/stacks-integrate-alignments -> ../../stacks/bin/stacks-integrate-alignments lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/stacks-samtools-tview -> ../../stacks/bin/stacks-samtools-tview lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/tsv2bam -> ../../stacks/bin/tsv2bam lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/debian-med/bin/ustacks -> ../../stacks/bin/ustacks drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/stacks/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/lib/stacks/bin/ -rwxr-xr-x root/root 297704 2020-04-25 23:41 ./usr/lib/stacks/bin/clone_filter -rwxr-xr-x root/root 8652 2020-04-25 23:41 ./usr/lib/stacks/bin/count_fixed_catalog_snps.py -rwxr-xr-x root/root 383548 2020-04-25 23:41 ./usr/lib/stacks/bin/cstacks lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/stacks/bin/denovo_map -> denovo_map.pl -rwxr-xr-x root/root 30259 2020-04-25 23:41 ./usr/lib/stacks/bin/denovo_map.pl -rwxr-xr-x root/root 657672 2020-04-25 23:41 ./usr/lib/stacks/bin/gstacks -rwxr-xr-x root/root 10879 2020-04-25 23:41 ./usr/lib/stacks/bin/integrate_alignments.py -rwxr-xr-x root/root 248528 2020-04-25 23:41 ./usr/lib/stacks/bin/kmer_filter -rwxr-xr-x root/root 309848 2020-04-25 23:41 ./usr/lib/stacks/bin/phasedstacks -rwxr-xr-x root/root 860200 2020-04-25 23:41 ./usr/lib/stacks/bin/populations -rwxr-xr-x root/root 356312 2020-04-25 23:41 ./usr/lib/stacks/bin/process_radtags -rwxr-xr-x root/root 314532 2020-04-25 23:41 ./usr/lib/stacks/bin/process_shortreads lrwxrwxrwx root/root 0 2020-04-25 23:41 ./usr/lib/stacks/bin/ref_map -> ref_map.pl -rwxr-xr-x root/root 15168 2020-04-25 23:41 ./usr/lib/stacks/bin/ref_map.pl -rwxr-xr-x root/root 371160 2020-04-25 23:41 ./usr/lib/stacks/bin/sstacks -rwxr-xr-x root/root 757 2020-04-25 23:41 ./usr/lib/stacks/bin/stacks-count-reads-per-sample-per-locus -rwxr-xr-x root/root 773 2020-04-25 23:41 ./usr/lib/stacks/bin/stacks-dist-extract -rwxr-xr-x root/root 1207 2020-04-25 23:41 ./usr/lib/stacks/bin/stacks-gdb -rwxr-xr-x root/root 1773 2020-04-25 23:41 ./usr/lib/stacks/bin/stacks-hist2d-loci-samples-coverage -rwxr-xr-x root/root 5752 2020-04-25 23:41 ./usr/lib/stacks/bin/stacks-integrate-alignments -rwxr-xr-x root/root 3037 2020-04-25 23:41 ./usr/lib/stacks/bin/stacks-samtools-tview -rwxr-xr-x root/root 362636 2020-04-25 23:41 ./usr/lib/stacks/bin/tsv2bam -rwxr-xr-x root/root 400368 2020-04-25 23:41 ./usr/lib/stacks/bin/ustacks drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/share/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/share/doc/ drwxr-xr-x root/root 0 2020-04-25 23:41 ./usr/share/doc/stacks/ -rw-r--r-- root/root 1451 2020-03-26 01:24 ./usr/share/doc/stacks/README.Debian -rw-r--r-- root/root 1749 2020-04-25 23:41 ./usr/share/doc/stacks/changelog.Debian.gz -rw-r--r-- root/root 28518 2020-03-28 23:10 ./usr/share/doc/stacks/changelog.gz -rw-r--r-- root/root 1684 2020-04-25 23:41 ./usr/share/doc/stacks/copyright lintian ------- Setup apt archive ----------------- Merged Build-Depends: lintian:amd64 Filtered Build-Depends: lintian:amd64 dpkg-deb: building package 'sbuild-build-depends-lintian-dummy' in '/<>/apt_archive/sbuild-build-depends-lintian-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [963 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [561 B] Get:5 copy:/<>/apt_archive ./ Packages [649 B] Fetched 2173 B in 0s (143 kB/s) Reading package lists... Reading package lists... Install lintian build dependencies (apt-based resolver) ------------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcpanel-json-xs-perl libdevel-callchecker-perl libdevel-size-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-socket-ssl-perl libipc-system-simple-perl libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxml-writer-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common t1utils Suggested packages: libxml-parser-perl libdata-dump-perl ca-certificates libscalar-number-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-lexalias-perl libdevel-stacktrace-perl libwww-perl binutils-multiarch libtext-template-perl readline-doc Recommended packages: gnupg libhttp-message-perl libasync-mergepoint-perl libsereal-perl libtest-fatal-perl libtest-refcount-perl libdigest-bubblebabble-perl libnet-dns-sec-perl libnet-libidn-perl libperl4-corelibs-perl libauthen-sasl-perl libpackage-stash-xs-perl libref-util-perl libtype-tiny-xs-perl libperlio-gzip-perl The following NEW packages will be installed: diffstat gpg gpgconf libapt-pkg-perl libassuan0 libb-hooks-endofscope-perl libb-hooks-op-check-perl libcapture-tiny-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcpanel-json-xs-perl libdevel-callchecker-perl libdevel-size-perl libdigest-hmac-perl libdynaloader-functions-perl libemail-valid-perl libexporter-tiny-perl libfile-basedir-perl libfile-find-rule-perl libfont-ttf-perl libfuture-perl libhtml-parser-perl libhtml-tagset-perl libimport-into-perl libio-async-loop-epoll-perl libio-async-perl libio-socket-ssl-perl libipc-system-simple-perl libjson-maybexs-perl liblinux-epoll-perl liblist-compare-perl liblist-moreutils-perl libmailtools-perl libmodule-implementation-perl libmodule-runtime-perl libmoo-perl libmoox-aliases-perl libnamespace-clean-perl libnet-dns-perl libnet-domain-tld-perl libnet-ip-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnumber-compare-perl libpackage-stash-perl libparams-classify-perl libpath-tiny-perl libreadline8 librole-tiny-perl libsereal-decoder-perl libsereal-encoder-perl libsqlite3-0 libssl1.1 libstrictures-perl libstruct-dumb-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-name-perl libsub-quote-perl libtext-glob-perl libtext-levenshtein-perl libtimedate-perl libtry-tiny-perl libtype-tiny-perl libunicode-utf8-perl liburi-perl libvariable-magic-perl libxml-writer-perl libyaml-0-2 libyaml-libyaml-perl lintian netbase patchutils perl-openssl-defaults readline-common sbuild-build-depends-lintian-dummy:armel t1utils 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 9224 kB of archives. After this operation, 26.3 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-lintian-dummy 0.invalid.0 [848 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-4 [72.5 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-4 [160 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 netbase all 6.1 [19.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 diffstat amd64 1.63-1 [35.6 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libassuan0 amd64 2.5.3-7 [50.4 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 gpgconf amd64 2.2.20-1 [532 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.31.1-5 [661 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 gpg amd64 2.2.20-1 [894 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libapt-pkg-perl amd64 0.1.36+b3 [71.0 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libb-hooks-op-check-perl amd64 0.22-1+b2 [11.3 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 libdynaloader-functions-perl all 0.003-1 [12.6 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 libdevel-callchecker-perl amd64 0.008-1+b1 [15.9 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 libparams-classify-perl amd64 0.015-1+b2 [25.6 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-runtime-perl all 0.016-1 [19.4 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libvariable-magic-perl amd64 0.62-1+b2 [46.0 kB] Get:20 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unstable/main amd64 liblist-moreutils-perl amd64 0.416-1+b5 [63.6 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 librole-tiny-perl all 2.001004-1 [20.8 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 libstrictures-perl all 2.000006-1 [18.6 kB] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-quote-perl all 2.006006-1 [21.0 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libmoo-perl all 2.004000-1 [59.4 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libmoox-aliases-perl all 0.001006-1 [10.2 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 libpackage-stash-perl all 0.38-1 [21.7 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-identify-perl amd64 0.14-1+b2 [12.0 kB] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-name-perl amd64 0.26-1 [13.5 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libpath-tiny-perl all 0.112-1 [53.5 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-decoder-perl amd64 4.011+ds-1 [106 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libsereal-encoder-perl amd64 4.011+ds-1 [108 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libtext-levenshtein-perl all 0.13-1 [11.1 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libtype-tiny-perl all 1.010001-1 [338 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libunicode-utf8-perl amd64 0.62-1+b1 [20.2 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-libyaml-perl amd64 0.82+repack-1 [35.6 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 patchutils amd64 0.3.4-2+b1 [91.4 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 lintian all 2.71.0 [1287 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9224 kB in 0s (47.4 MB/s) Selecting previously unselected package readline-common. (Reading database ... 20417 files and directories currently installed.) Preparing to unpack .../00-readline-common_8.0-4_all.deb ... Unpacking readline-common (8.0-4) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../01-libreadline8_8.0-4_amd64.deb ... Unpacking libreadline8:amd64 (8.0-4) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.1_all.deb ... Unpacking netbase (6.1) ... Selecting previously unselected package diffstat. Preparing to unpack .../03-diffstat_1.63-1_amd64.deb ... Unpacking diffstat (1.63-1) ... Selecting previously unselected package libassuan0:amd64. Preparing to unpack .../04-libassuan0_2.5.3-7_amd64.deb ... Unpacking libassuan0:amd64 (2.5.3-7) ... Selecting previously unselected package gpgconf. Preparing to unpack .../05-gpgconf_2.2.20-1_amd64.deb ... Unpacking gpgconf (2.2.20-1) ... Selecting previously unselected package libsqlite3-0:amd64. 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Setting up libjson-maybexs-perl (1.004001-1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libdigest-hmac-perl (1.03+dfsg-2) ... Setting up libipc-system-simple-perl (1.30-1) ... Setting up libnet-domain-tld-perl (1.75-1) ... Setting up libxml-writer-perl (0.625-1) ... Setting up t1utils (1.41-4) ... Setting up liblinux-epoll-perl (0.017-1) ... Setting up diffstat (1.63-1) ... Setting up libvariable-magic-perl (0.62-1+b2) ... Setting up libb-hooks-op-check-perl (0.22-1+b2) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libcapture-tiny-perl (0.48-1) ... Setting up libtimedate-perl (2.3200-1) ... Setting up libsub-name-perl (0.26-1) ... Setting up libpath-tiny-perl (0.112-1) ... Setting up librole-tiny-perl (2.001004-1) ... Setting up netbase (6.1) ... Setting up libstrictures-perl (2.000006-1) ... Setting up libsub-quote-perl (2.006006-1) ... Setting up libclass-xsaccessor-perl (1.19-3+b3) ... Setting up libexporter-tiny-perl (1.002001-1) ... Setting up libfont-ttf-perl (1.06-1) ... Setting up libnet-ip-perl (1.26-2) ... Setting up readline-common (8.0-4) ... Setting up libsereal-decoder-perl (4.011+ds-1) ... Setting up liburi-perl (1.76-2) ... Setting up libnet-ssleay-perl (1.88-3) ... Setting up libfile-basedir-perl (0.08-1) ... Setting up liblist-moreutils-perl (0.416-1+b5) ... Setting up libreadline8:amd64 (8.0-4) ... Setting up libtype-tiny-perl (1.010001-1) ... Setting up libnet-dns-perl (1.23-1) ... Setting up libdevel-callchecker-perl (0.008-1+b1) ... Setting up libio-async-loop-epoll-perl (0.20-1) ... Setting up libhtml-parser-perl (3.72-5) ... Setting up gpgconf (2.2.20-1) ... Setting up libio-socket-ssl-perl (2.067-1) ... Setting up gpg (2.2.20-1) ... Setting up libparams-classify-perl (0.015-1+b2) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libmodule-runtime-perl (0.016-1) ... Setting up libmailtools-perl (2.21-1) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libemail-valid-perl (1.202-1) ... Setting up libpackage-stash-perl (0.38-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libmoo-perl (2.004000-1) ... Setting up libmoox-aliases-perl (0.001006-1) ... Setting up libb-hooks-endofscope-perl (0.24-1) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up lintian (2.71.0) ... Setting up sbuild-build-depends-lintian-dummy:armel (0.invalid.0) ... Processing triggers for man-db (2.9.1-1) ... Not building database; man-db/auto-update is not 'true'. Processing triggers for libc-bin (2.30-7) ... I: Lintian run was successful. +------------------------------------------------------------------------------+ | Post Build | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 331908 Build-Time: 325 Distribution: unstable Foreign Architectures: armel Host Architecture: armel Install-Time: 19 Job: stacks_2.53+dfsg-1 Lintian: pass Machine Architecture: amd64 Package: stacks Package-Time: 354 Source-Version: 2.53+dfsg-1 Space: 331908 Status: successful Version: 2.53+dfsg-1 -------------------------------------------------------------------------------- Finished at 2020-05-06T21:06:26Z Build needed 00:05:54, 331908k disk space