Mon Apr 10 20:06:02 UTC 2023 I: starting to build sambamba/bookworm/arm64 on jenkins on '2023-04-10 20:05' Mon Apr 10 20:06:02 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_21/21720/console.log Mon Apr 10 20:06:02 UTC 2023 I: Downloading source for bookworm/sambamba=1.0+dfsg-1 --2023-04-10 20:06:03-- http://cdn-fastly.deb.debian.org/debian/pool/main/s/sambamba/sambamba_1.0%2bdfsg-1.dsc Connecting to 78.137.99.97:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2224 (2.2K) [text/prs.lines.tag] Saving to: ‘sambamba_1.0+dfsg-1.dsc’ 0K .. 100% 188M=0s 2023-04-10 20:06:03 (188 MB/s) - ‘sambamba_1.0+dfsg-1.dsc’ saved [2224/2224] Mon Apr 10 20:06:03 UTC 2023 I: sambamba_1.0+dfsg-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: sambamba Binary: sambamba Architecture: any Version: 1.0+dfsg-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/lomereiter/sambamba Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/sambamba Vcs-Git: https://salsa.debian.org/med-team/sambamba.git Testsuite: autopkgtest Testsuite-Triggers: shunit2 Build-Depends: debhelper-compat (= 13), dh-dlang, libhts-dev (>= 1.10.2-4), meson, pkg-config, python3, shunit2 , zlib1g-dev, ldc, liblz4-dev, libcurl4-gnutls-dev | libcurl-dev, libssl-dev, libbz2-dev, libdeflate-dev, liblzma-dev, debhelper Package-List: sambamba deb science optional arch=any Checksums-Sha1: 83b57b46dfefec1cb2a2b616e50baa220524ebf9 451508 sambamba_1.0+dfsg.orig.tar.xz 0bad6ecbb60d305736aaf8ccd3a42d2b810e98d9 7940 sambamba_1.0+dfsg-1.debian.tar.xz Checksums-Sha256: 48cbace1dedec9e1a662514beb3a80ad50a7d9f44e4efb49794c86ab0572e8fe 451508 sambamba_1.0+dfsg.orig.tar.xz 64e542f532752bf6c5a88f8ac3d809067aed82362bd61c89ce8ff5dc18940550 7940 sambamba_1.0+dfsg-1.debian.tar.xz Files: ed92fc218f9a61ec618fb463fff1ad71 451508 sambamba_1.0+dfsg.orig.tar.xz dbd504a2004b2ad766929741c25dd084 7940 sambamba_1.0+dfsg-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmPJKdQRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHk+hAAi5W0Ji1Eq/RmGGdKDkuPwdugAvHRHK7O rxuEiKRWZyUooHXzKD/DL1wRZQPrO9QL5GkB+CE27AgLtCdub5r7g+qWxbl5dpe8 LYkEemiDPHYgttCTPSUM5rEaxn9NG/Uw2+hEhM9/Oijf8W8DHm4AUWm1uNGhG6iE 1MDG7kjFN/6OQ+DdxoY3wNlfUnS/kam8HCXhPyyHfBn+v2Lge3mnkc11GbzWc4Wm WJ/Hs3oxTdhG73z3pdIM+Xla0Cgs9pawurmDrJbMcJ8fHMof1eykbDz5+eM6qYEp zNfzgGTXGz7OxzByqLdeTeaDGSVGXCLWvUX0tSCbH+cuzVA2jFhtW9X2466uors5 ak/fCpK0rPtjWXVn676eWldgVNXJrbSOtPxRd+uE80tAukWuzo0kkJP2ANYcHyqo 8Qb10ryLcffJtjHKOG4TKYYLh8plHIyUApyIazq4H2yOFM6cPXU0uSzft6uDpxcv vxqSpHgd+yL03unsp4yOOlfXmLhlZ1KjLrGToOtVGuGomj90oIaYlzbhTFkzLB/s wBsQzoTqnaevEXsUKCTAvAxp01sm5ju0IjO02Mq+ltosJo70ErnU2njQA0v9zYLA CejBzCZ/m3oY/7OSRq0wBPz1cY3iVmE9OTmK9d7bAm5epS75ZeOiSnokeRtvhPqF jtTH0pPiAk8= =JUX9 -----END PGP SIGNATURE----- Mon Apr 10 20:06:03 UTC 2023 I: Checking whether the package is not for us Mon Apr 10 20:06:03 UTC 2023 I: Starting 1st build on remote node codethink14-arm64.debian.net. Mon Apr 10 20:06:03 UTC 2023 I: Preparing to do remote build '1' on codethink14-arm64.debian.net. Mon Apr 10 20:14:15 UTC 2023 I: Deleting $TMPDIR on codethink14-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Mon Apr 10 08:06:06 -12 2023 I: pbuilder-time-stamp: 1681157166 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [sambamba_1.0+dfsg-1.dsc] I: copying [./sambamba_1.0+dfsg.orig.tar.xz] I: copying [./sambamba_1.0+dfsg-1.debian.tar.xz] I: Extracting source gpgv: Signature made Wed Jan 18 23:30:28 2023 -12 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./sambamba_1.0+dfsg-1.dsc: no acceptable signature found dpkg-source: info: extracting sambamba in sambamba-1.0+dfsg dpkg-source: info: unpacking sambamba_1.0+dfsg.orig.tar.xz dpkg-source: info: unpacking sambamba_1.0+dfsg-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 2to3.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/11426/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='11426' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.WvUsql4p/pbuilderrc_i9lP --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WvUsql4p/b1 --logfile b1/build.log sambamba_1.0+dfsg-1.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink14-arm64 4.15.0-208-generic #220-Ubuntu SMP Mon Mar 20 14:28:12 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Apr 9 22:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/11426/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), dh-dlang, libhts-dev (>= 1.10.2-4), meson, pkg-config, python3, shunit2, zlib1g-dev, ldc, liblz4-dev, libcurl4-gnutls-dev | libcurl-dev, libssl-dev, libbz2-dev, libdeflate-dev, liblzma-dev, debhelper dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19616 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-dlang; however: Package dh-dlang is not installed. pbuilder-satisfydepends-dummy depends on libhts-dev (>= 1.10.2-4); however: Package libhts-dev is not installed. pbuilder-satisfydepends-dummy depends on meson; however: Package meson is not installed. pbuilder-satisfydepends-dummy depends on pkg-config; however: Package pkg-config is not installed. pbuilder-satisfydepends-dummy depends on python3; however: Package python3 is not installed. pbuilder-satisfydepends-dummy depends on shunit2; however: Package shunit2 is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. pbuilder-satisfydepends-dummy depends on ldc; however: Package ldc is not installed. pbuilder-satisfydepends-dummy depends on liblz4-dev; however: Package liblz4-dev is not installed. pbuilder-satisfydepends-dummy depends on libcurl4-gnutls-dev | libcurl-dev; however: Package libcurl4-gnutls-dev is not installed. Package libcurl-dev is not installed. pbuilder-satisfydepends-dummy depends on libssl-dev; however: Package libssl-dev is not installed. pbuilder-satisfydepends-dummy depends on libbz2-dev; however: Package libbz2-dev is not installed. pbuilder-satisfydepends-dummy depends on libdeflate-dev; however: Package libdeflate-dev is not installed. pbuilder-satisfydepends-dummy depends on liblzma-dev; however: Package liblzma-dev is not installed. pbuilder-satisfydepends-dummy depends on debhelper; however: Package debhelper is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} default-d-compiler{a} dh-autoreconf{a} dh-dlang{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} ldc{a} libarchive-zip-perl{a} libbrotli1{a} libbsd0{a} libbz2-dev{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libedit2{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libhts-dev{a} libhts3{a} libhtscodecs2{a} libicu72{a} libldap-2.5-0{a} libllvm14{a} liblz4-dev{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libnghttp2-14{a} libphobos2-ldc-shared-dev{a} libphobos2-ldc-shared100{a} libpipeline1{a} libpkgconf3{a} libpsl5{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1{a} libssl-dev{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libz3-4{a} m4{a} man-db{a} media-types{a} meson{a} ninja-build{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3-pkg-resources{a} python3-setuptools{a} python3.11{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} shunit2{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: bzip2-doc ca-certificates curl libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix wget 0 packages upgraded, 81 newly installed, 0 to remove and 0 not upgraded. Need to get 69.2 MB of archives. After unpacking 342 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1 [26.0 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1 [9012 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1 [26.0 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 32 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libphobos2-ldc-shared100 arm64 1:1.30.0-1+b1 [1145 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libphobos2-ldc-shared-dev arm64 1:1.30.0-1+b1 [6246 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libz3-4 arm64 4.8.12-3.1 [6282 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libllvm14 arm64 1:14.0.6-12 [19.3 MB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 ldc arm64 1:1.30.0-1+b1 [3090 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 default-d-compiler arm64 0.6.5 [3020 B] Get: 50 http://deb.debian.org/debian bookworm/main arm64 dh-dlang all 0.6.5 [5020 B] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 libbz2-dev arm64 1.0.8-5+b1 [31.5 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libcurl3-gnutls arm64 7.88.1-7 [356 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libcurl4-gnutls-dev arm64 7.88.1-7 [466 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libhtscodecs2 arm64 1.3.0-4 [70.5 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libhts3 arm64 1.16+ds-3 [392 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libhts-dev arm64 1.16+ds-3 [1525 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 liblz4-dev arm64 1.9.4-1 [81.9 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libssl-dev arm64 3.0.8-1 [2296 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 ninja-build arm64 1.11.1-1 [127 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-2 [76.2 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-2 [131 kB] Get: 76 http://deb.debian.org/debian bookworm/main arm64 python3-setuptools all 66.1.1-1 [521 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 meson all 1.0.1-5 [548 kB] Get: 78 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 shunit2 all 2.1.8-3 [33.6 kB] Fetched 69.2 MB in 3s (19.9 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. 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Setting up python3-setuptools (66.1.1-1) ... Setting up meson (1.0.1-5) ... Processing triggers for libc-bin (2.36-8) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/sambamba-1.0+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../sambamba_1.0+dfsg-1_source.changes dpkg-buildpackage: info: source package sambamba dpkg-buildpackage: info: source version 1.0+dfsg-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean mkdir -p obj-aarch64-linux-gnu dh clean --buildsystem=meson debian/rules override_dh_auto_clean make[1]: Entering directory '/build/sambamba-1.0+dfsg' dh_auto_clean rm -rf /build/sambamba-1.0+dfsg/output/ rm -f test.log make[1]: Leaving directory '/build/sambamba-1.0+dfsg' dh_autoreconf_clean -O--buildsystem=meson dh_clean -O--buildsystem=meson debian/rules binary mkdir -p obj-aarch64-linux-gnu dh binary --buildsystem=meson dh_update_autotools_config -O--buildsystem=meson dh_autoreconf -O--buildsystem=meson debian/rules override_dh_auto_configure make[1]: Entering directory '/build/sambamba-1.0+dfsg' dh_auto_configure -- -Doptimize_strong=true -Dcpp_link_args="-wi -L=-z -L=relro /usr/lib/x86_64-linux-gnu/libhts.a -L=-lz -L=-lcrypto -L=-lcurl -L=-llzma -L=-lbz2 -L=-ldeflate -L=-llz4" cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 meson setup .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/aarch64-linux-gnu -Doptimize_strong=true "-Dcpp_link_args=-wi -L=-z -L=relro /usr/lib/x86_64-linux-gnu/libhts.a -L=-lz -L=-lcrypto -L=-lcurl -L=-llzma -L=-lbz2 -L=-ldeflate -L=-llz4" The Meson build system Version: 1.0.1 Source dir: /build/sambamba-1.0+dfsg Build dir: /build/sambamba-1.0+dfsg/obj-aarch64-linux-gnu Build type: native build Project name: Sambamba Project version: 0.8.2 C compiler for the host machine: cc (gcc 12.2.0 "cc (Debian 12.2.0-14) 12.2.0") C linker for the host machine: cc ld.bfd 2.40 D compiler for the host machine: ldc2 (llvm 1.30.0 "LDC - the LLVM D compiler (1.30.0):") D linker for the host machine: ldc2 ld.bfd 2.40 Host machine cpu family: aarch64 Host machine cpu: aarch64 Found pkg-config: /usr/bin/pkg-config (1.8.1) Run-time dependency liblz4 found: YES 1.9.4 Run-time dependency zlib found: YES 1.2.13 Program ldc2 found: YES (/usr/bin/ldc2) Program mkdir found: YES (/usr/bin/mkdir) WARNING: You should add the boolean check kwarg to the run_command call. It currently defaults to false, but it will default to true in future releases of meson. See also: https://github.com/mesonbuild/meson/issues/9300 Program /build/sambamba-1.0+dfsg/test/test_suite.sh found: YES (/build/sambamba-1.0+dfsg/test/test_suite.sh) Build targets in project: 1 Sambamba 0.8.2 User defined options buildtype : plain libdir : lib/aarch64-linux-gnu localstatedir : /var prefix : /usr sysconfdir : /etc wrap_mode : nodownload cpp_link_args : -wi -L=-z -L=relro /usr/lib/x86_64-linux-gnu/libhts.a -L=-lz -L=-lcrypto -L=-lcurl -L=-llzma -L=-lbz2 -L=-ldeflate -L=-llz4 optimize_strong: true Found ninja-1.11.1 at /usr/bin/ninja make[1]: Leaving directory '/build/sambamba-1.0+dfsg' dh_auto_build -O--buildsystem=meson cd obj-aarch64-linux-gnu && LC_ALL=C.UTF-8 ninja -j8 -v [1/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_main.d.o.deps -of=sambamba.p/sambamba_main.d.o -c ../sambamba/main.d [2/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_markdup2.d.o.deps -of=sambamba.p/sambamba_markdup2.d.o -c ../sambamba/markdup2.d [3/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_index.d.o.deps -of=sambamba.p/sambamba_index.d.o -c ../sambamba/index.d [4/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_fixbins.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d [5/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_subsample.d.o.deps -of=sambamba.p/sambamba_subsample.d.o -c ../sambamba/subsample.d [6/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_slice.d.o.deps -of=sambamba.p/sambamba_slice.d.o -c ../sambamba/slice.d [7/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_file.d.o.deps -of=sambamba.p/sambamba_utils_common_file.d.o -c ../sambamba/utils/common/file.d [8/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_flagstat.d.o.deps -of=sambamba.p/sambamba_flagstat.d.o -c ../sambamba/flagstat.d [9/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_intervaltree.d.o.deps -of=sambamba.p/sambamba_utils_common_intervaltree.d.o -c ../sambamba/utils/common/intervaltree.d [10/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_merge.d.o.deps -of=sambamba.p/sambamba_merge.d.o -c ../sambamba/merge.d [11/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_overwrite.d.o.deps -of=sambamba.p/sambamba_utils_common_overwrite.d.o -c ../sambamba/utils/common/overwrite.d [12/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_pratt_parser.d.o.deps -of=sambamba.p/sambamba_utils_common_pratt_parser.d.o -c ../sambamba/utils/common/pratt_parser.d [13/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_bed.d.o.deps -of=sambamba.p/sambamba_utils_common_bed.d.o -c ../sambamba/utils/common/bed.d [14/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_ldc_gc_workaround.d.o.deps -of=sambamba.p/sambamba_utils_common_ldc_gc_workaround.d.o -c ../sambamba/utils/common/ldc_gc_workaround.d [15/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_readstorage.d.o.deps -of=sambamba.p/sambamba_utils_common_readstorage.d.o -c ../sambamba/utils/common/readstorage.d [16/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_sort.d.o.deps -of=sambamba.p/sambamba_sort.d.o -c ../sambamba/sort.d [17/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_view_alignmentrangeprocessor.d.o.deps -of=sambamba.p/sambamba_utils_view_alignmentrangeprocessor.d.o -c ../sambamba/utils/view/alignmentrangeprocessor.d [18/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_tmpdir.d.o.deps -of=sambamba.p/sambamba_utils_common_tmpdir.d.o -c ../sambamba/utils/common/tmpdir.d [19/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_depth.d.o.deps -of=sambamba.p/sambamba_depth.d.o -c ../sambamba/depth.d ../BioD/bio/std/hts/bam/md/parse.d(49): Deprecation: returning `this._cached_front` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/parse.d(48): perhaps annotate the function with `return` ../BioD/bio/std/hts/bam/md/parse.d(53): Deprecation: returning `this._cached_back` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/parse.d(52): perhaps annotate the function with `return` [20/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_validate.d.o.deps -of=sambamba.p/sambamba_validate.d.o -c ../sambamba/validate.d [21/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_base.d.o.deps -of=sambamba.p/BioD_bio_core_base.d.o -c ../BioD/bio/core/base.d [22/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_progressbar.d.o.deps -of=sambamba.p/sambamba_utils_common_progressbar.d.o -c ../sambamba/utils/common/progressbar.d [23/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_bgzf_chunk.d.o.deps -of=sambamba.p/BioD_bio_core_bgzf_chunk.d.o -c ../BioD/bio/core/bgzf/chunk.d [24/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_bgzf_block.d.o.deps -of=sambamba.p/BioD_bio_core_bgzf_block.d.o -c ../BioD/bio/core/bgzf/block.d [25/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_markdup.d.o.deps -of=sambamba.p/sambamba_markdup.d.o -c ../sambamba/markdup.d [26/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_bgzf_constants.d.o.deps -of=sambamba.p/BioD_bio_core_bgzf_constants.d.o -c ../BioD/bio/core/bgzf/constants.d [27/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_bgzf_compress.d.o.deps -of=sambamba.p/BioD_bio_core_bgzf_compress.d.o -c ../BioD/bio/core/bgzf/compress.d [28/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_bgzf_outputstream.d.o.deps -of=sambamba.p/BioD_bio_core_bgzf_outputstream.d.o -c ../BioD/bio/core/bgzf/outputstream.d [29/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_call.d.o.deps -of=sambamba.p/BioD_bio_core_call.d.o -c ../BioD/bio/core/call.d [30/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_decompress.d.o.deps -of=sambamba.p/BioD_bio_core_decompress.d.o -c ../BioD/bio/core/decompress.d [31/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_bgzf_virtualoffset.d.o.deps -of=sambamba.p/BioD_bio_core_bgzf_virtualoffset.d.o -c ../BioD/bio/core/bgzf/virtualoffset.d [32/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_kmer.d.o.deps -of=sambamba.p/BioD_bio_core_kmer.d.o -c ../BioD/bio/core/kmer.d [33/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_genotype.d.o.deps -of=sambamba.p/BioD_bio_core_genotype.d.o -c ../BioD/bio/core/genotype.d [34/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_region.d.o.deps -of=sambamba.p/BioD_bio_core_region.d.o -c ../BioD/bio/core/region.d [35/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_tinymap.d.o.deps -of=sambamba.p/BioD_bio_core_tinymap.d.o -c ../BioD/bio/core/tinymap.d [36/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_sequence.d.o.deps -of=sambamba.p/BioD_bio_core_sequence.d.o -c 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-J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_memoize.d.o.deps -of=sambamba.p/BioD_bio_core_utils_memoize.d.o -c ../BioD/bio/core/utils/memoize.d [41/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_bgzf_inputstream.d.o.deps -of=sambamba.p/BioD_bio_core_bgzf_inputstream.d.o -c ../BioD/bio/core/bgzf/inputstream.d [42/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_outbuffer.d.o.deps -of=sambamba.p/BioD_bio_core_utils_outbuffer.d.o -c ../BioD/bio/core/utils/outbuffer.d [43/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_bylinefast.d.o.deps -of=sambamba.p/BioD_bio_core_utils_bylinefast.d.o -c ../BioD/bio/core/utils/bylinefast.d [44/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_range.d.o.deps -of=sambamba.p/BioD_bio_core_utils_range.d.o -c ../BioD/bio/core/utils/range.d [45/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_roundbuf.d.o.deps -of=sambamba.p/BioD_bio_core_utils_roundbuf.d.o -c ../BioD/bio/core/utils/roundbuf.d [46/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_switchendianness.d.o.deps -of=sambamba.p/BioD_bio_core_utils_switchendianness.d.o -c ../BioD/bio/core/utils/switchendianness.d [47/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_zlib.d.o.deps -of=sambamba.p/BioD_bio_core_utils_zlib.d.o -c ../BioD/bio/core/utils/zlib.d [48/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_stream.d.o.deps -of=sambamba.p/BioD_bio_core_utils_stream.d.o -c ../BioD/bio/core/utils/stream.d ../BioD/bio/core/utils/stream.d(32): Deprecation: switch case fallthrough - use 'goto case;' if intended [49/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_bam_header.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_bam_header.d.o -c ../BioD/bio/std/experimental/hts/bam/header.d [50/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_core_utils_tmpfile.d.o.deps -of=sambamba.p/BioD_bio_core_utils_tmpfile.d.o -c ../BioD/bio/core/utils/tmpfile.d [51/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_bam_writer.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_bam_writer.d.o -c ../BioD/bio/std/experimental/hts/bam/writer.d [52/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_view_headerserializer.d.o.deps -of=sambamba.p/sambamba_utils_view_headerserializer.d.o -c ../sambamba/utils/view/headerserializer.d [53/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_constants.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_constants.d.o -c ../BioD/bio/std/experimental/hts/constants.d [54/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_bgzf_writer.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_bgzf_writer.d.o -c ../BioD/bio/std/experimental/hts/bgzf_writer.d [55/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_logger.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_logger.d.o -c ../BioD/bio/std/experimental/hts/logger.d [56/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_hashing.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_hashing.d.o -c ../BioD/bio/std/experimental/hts/hashing.d [57/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_reads.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_reads.d.o -c ../BioD/bio/std/experimental/hts/reads.d [58/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_pileup.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_pileup.d.o -c ../BioD/bio/std/experimental/hts/pileup.d [59/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_filtering.d.o.deps -of=sambamba.p/sambamba_utils_common_filtering.d.o -c ../sambamba/utils/common/filtering.d [60/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_unpack.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_unpack.d.o -c ../BioD/bio/std/experimental/hts/unpack.d [61/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_file_fastq.d.o.deps -of=sambamba.p/BioD_bio_std_file_fastq.d.o -c ../BioD/bio/std/file/fastq.d [62/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_genotype_maf.d.o.deps -of=sambamba.p/BioD_bio_std_genotype_maf.d.o -c ../BioD/bio/std/genotype/maf.d [63/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_bgzf.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_bgzf.d.o -c ../BioD/bio/std/experimental/hts/bgzf.d ../BioD/bio/std/experimental/hts/bgzf.d(91): Deprecation: package bio.core.utils is not accessible here, perhaps add 'static import bio.core.utils;' ../BioD/bio/std/experimental/hts/bgzf.d(91): Deprecation: module bio.core.utils.zlib is not accessible here, perhaps add 'static import bio.core.utils.zlib;' [64/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_abstractreader.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_abstractreader.d.o -c ../BioD/bio/std/hts/bam/abstractreader.d [65/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_bai_bin.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_bai_bin.d.o -c ../BioD/bio/std/hts/bam/bai/bin.d [66/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_experimental_hts_bam_reader.d.o.deps -of=sambamba.p/BioD_bio_std_experimental_hts_bam_reader.d.o -c ../BioD/bio/std/experimental/hts/bam/reader.d [67/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_baifile.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_baifile.d.o -c ../BioD/bio/std/hts/bam/baifile.d [68/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_baseinfo.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_baseinfo.d.o -c ../BioD/bio/std/hts/bam/baseinfo.d [69/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_cigar.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_cigar.d.o -c ../BioD/bio/std/hts/bam/cigar.d [70/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_constants.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_constants.d.o -c ../BioD/bio/std/hts/bam/constants.d [71/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_md_core.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_md_core.d.o -c ../BioD/bio/std/hts/bam/md/core.d [72/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_file_fai.d.o.deps -of=sambamba.p/BioD_bio_std_file_fai.d.o -c ../BioD/bio/std/file/fai.d [73/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_view.d.o.deps -of=sambamba.p/sambamba_view.d.o -c ../sambamba/view.d [74/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_md_reconstruct.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_md_reconstruct.d.o -c ../BioD/bio/std/hts/bam/md/reconstruct.d [75/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_md_parse.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_md_parse.d.o -c ../BioD/bio/std/hts/bam/md/parse.d ../BioD/bio/std/hts/bam/md/parse.d(49): Deprecation: returning `this._cached_front` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/parse.d(48): perhaps annotate the function with `return` ../BioD/bio/std/hts/bam/md/parse.d(53): Deprecation: returning `this._cached_back` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/parse.d(52): perhaps annotate the function with `return` [76/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_file_fasta.d.o.deps -of=sambamba.p/BioD_bio_std_file_fasta.d.o -c ../BioD/bio/std/file/fasta.d [77/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_pileup.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_pileup.d.o -c ../BioD/bio/std/hts/bam/pileup.d [78/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_genotype_snp.d.o.deps -of=sambamba.p/BioD_bio_std_genotype_snp.d.o -c ../BioD/bio/std/genotype/snp.d [79/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_pileup.d.o.deps -of=sambamba.p/sambamba_pileup.d.o -c ../sambamba/pileup.d ../BioD/bio/std/hts/bam/md/parse.d(49): Deprecation: returning `this._cached_front` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/parse.d(48): perhaps annotate the function with `return` ../BioD/bio/std/hts/bam/md/parse.d(53): Deprecation: returning `this._cached_back` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/parse.d(52): perhaps annotate the function with `return` [80/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_readrange.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_readrange.d.o -c ../BioD/bio/std/hts/bam/readrange.d [81/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/sambamba_utils_common_queryparser.d.o.deps -of=sambamba.p/sambamba_utils_common_queryparser.d.o -c ../sambamba/utils/common/queryparser.d [82/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_bai_indexing.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_bai_indexing.d.o -c ../BioD/bio/std/hts/bam/bai/indexing.d [83/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_region.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_region.d.o -c ../BioD/bio/std/hts/bam/region.d [84/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_referenceinfo.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_referenceinfo.d.o -c ../BioD/bio/std/hts/bam/referenceinfo.d [85/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_splitter.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_splitter.d.o -c ../BioD/bio/std/hts/bam/splitter.d [86/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_reference.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_reference.d.o -c ../BioD/bio/std/hts/bam/reference.d [87/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_randomaccessmanager.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_randomaccessmanager.d.o -c ../BioD/bio/std/hts/bam/randomaccessmanager.d [88/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_validation_samheader.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_validation_samheader.d.o -c ../BioD/bio/std/hts/bam/validation/samheader.d [89/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_md_operation.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_md_operation.d.o -c ../BioD/bio/std/hts/bam/md/operation.d ../BioD/bio/std/hts/bam/md/operation.d(57): Deprecation: returning `this._match` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/operation.d(56): perhaps annotate the function with `return` ../BioD/bio/std/hts/bam/md/operation.d(72): Deprecation: returning `this._deletion` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/operation.d(71): perhaps annotate the function with `return` [90/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_iontorrent_flowindex.d.o.deps -of=sambamba.p/BioD_bio_std_hts_iontorrent_flowindex.d.o -c ../BioD/bio/std/hts/iontorrent/flowindex.d [91/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_writer.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_writer.d.o -c ../BioD/bio/std/hts/bam/writer.d [92/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_reader.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_reader.d.o -c ../BioD/bio/std/hts/bam/reader.d [93/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_iontorrent_flowcall.d.o.deps -of=sambamba.p/BioD_bio_std_hts_iontorrent_flowcall.d.o -c ../BioD/bio/std/hts/iontorrent/flowcall.d [94/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_read.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_read.d.o -c ../BioD/bio/std/hts/bam/read.d ../BioD/bio/std/hts/bam/md/parse.d(49): Deprecation: returning `this._cached_front` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/parse.d(48): perhaps annotate the function with `return` ../BioD/bio/std/hts/bam/md/parse.d(53): Deprecation: returning `this._cached_back` escapes a reference to parameter `this` ../BioD/bio/std/hts/bam/md/parse.d(52): perhaps annotate the function with `return` [95/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_sam_reader.d.o.deps -of=sambamba.p/BioD_bio_std_hts_sam_reader.d.o -c ../BioD/bio/std/hts/sam/reader.d [96/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_snpcallers_maq.d.o.deps -of=sambamba.p/BioD_bio_std_hts_snpcallers_maq.d.o -c ../BioD/bio/std/hts/snpcallers/maq.d [97/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_snpcallers_simple.d.o.deps -of=sambamba.p/BioD_bio_std_hts_snpcallers_simple.d.o -c ../BioD/bio/std/hts/snpcallers/simple.d [98/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_utils_array.d.o.deps -of=sambamba.p/BioD_bio_std_hts_utils_array.d.o -c ../BioD/bio/std/hts/utils/array.d [99/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_tagvalue.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_tagvalue.d.o -c ../BioD/bio/std/hts/bam/tagvalue.d [100/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_utils_graph.d.o.deps -of=sambamba.p/BioD_bio_std_hts_utils_graph.d.o -c ../BioD/bio/std/hts/utils/graph.d [101/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_sam_utils_recordparser.d.o.deps -of=sambamba.p/BioD_bio_std_hts_sam_utils_recordparser.d.o -c ../BioD/bio/std/hts/sam/utils/recordparser.d sam_alignment.rl(51): Warning: statement is not reachable sam_alignment.rl(52): Warning: statement is not reachable sam_alignment.rl(59): Warning: statement is not reachable sam_alignment.rl(60): Warning: statement is not reachable sam_alignment.rl(68): Warning: statement is not reachable sam_alignment.rl(69): Warning: statement is not reachable sam_alignment.rl(76): Warning: statement is not reachable sam_alignment.rl(77): Warning: statement is not reachable sam_alignment.rl(82): Warning: statement is not reachable sam_alignment.rl(83): Warning: statement is not reachable sam_alignment.rl(131): Warning: statement is not reachable sam_alignment.rl(132): Warning: statement is not reachable sam_alignment.rl(163): Warning: statement is not reachable sam_alignment.rl(164): Warning: statement is not reachable sam_alignment.rl(176): Warning: statement is not reachable sam_alignment.rl(177): Warning: statement is not reachable sam_alignment.rl(188): Warning: statement is not reachable sam_alignment.rl(189): Warning: statement is not reachable sam_alignment.rl(221): Warning: statement is not reachable sam_alignment.rl(222): Warning: statement is not reachable sam_alignment.rl(250): Warning: statement is not reachable sam_alignment.rl(252): Warning: statement is not reachable sam_alignment.rl(407): Warning: statement is not reachable sam_alignment.rl(409): Warning: statement is not reachable sam_alignment.rl(51): Warning: statement is not reachable sam_alignment.rl(59): Warning: statement is not reachable sam_alignment.rl(68): Warning: statement is not reachable sam_alignment.rl(76): Warning: statement is not reachable sam_alignment.rl(82): Warning: statement is not reachable sam_alignment.rl(131): Warning: statement is not reachable sam_alignment.rl(163): Warning: statement is not reachable sam_alignment.rl(176): Warning: statement is not reachable sam_alignment.rl(188): Warning: statement is not reachable sam_alignment.rl(221): Warning: statement is not reachable sam_alignment.rl(250): Warning: statement is not reachable sam_alignment.rl(407): Warning: statement is not reachable [102/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_maf_block.d.o.deps -of=sambamba.p/BioD_bio_std_maf_block.d.o -c ../BioD/bio/std/maf/block.d [103/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_utils_value.d.o.deps -of=sambamba.p/BioD_bio_std_hts_utils_value.d.o -c ../BioD/bio/std/hts/utils/value.d [104/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_thirdparty_msgpack.d.o.deps -of=sambamba.p/BioD_bio_std_hts_thirdparty_msgpack.d.o -c ../BioD/bio/std/hts/thirdparty/msgpack.d [105/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_range_splitter.d.o.deps -of=sambamba.p/BioD_bio_std_range_splitter.d.o -c ../BioD/bio/std/range/splitter.d [106/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_sff_constants.d.o.deps -of=sambamba.p/BioD_bio_std_sff_constants.d.o -c ../BioD/bio/std/sff/constants.d [107/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_sff_index.d.o.deps -of=sambamba.p/BioD_bio_std_sff_index.d.o -c ../BioD/bio/std/sff/index.d [108/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_sff_read.d.o.deps -of=sambamba.p/BioD_bio_std_sff_read.d.o -c ../BioD/bio/std/sff/read.d [109/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_multireader.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_multireader.d.o -c ../BioD/bio/std/hts/bam/multireader.d [110/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_bam_validation_alignment.d.o.deps -of=sambamba.p/BioD_bio_std_hts_bam_validation_alignment.d.o -c ../BioD/bio/std/hts/bam/validation/alignment.d [111/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_maf_parser.d.o.deps -of=sambamba.p/BioD_bio_std_maf_parser.d.o -c ../BioD/bio/std/maf/parser.d [112/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_sff_utils_roundup.d.o.deps -of=sambamba.p/BioD_bio_std_sff_utils_roundup.d.o -c ../BioD/bio/std/sff/utils/roundup.d [113/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_sam_header.d.o.deps -of=sambamba.p/BioD_bio_std_hts_sam_header.d.o -c ../BioD/bio/std/hts/sam/header.d [114/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_sam_utils_fastrecordparser.d.o.deps -of=sambamba.p/BioD_bio_std_hts_sam_utils_fastrecordparser.d.o -c ../BioD/bio/std/hts/sam/utils/fastrecordparser.d sam_alignment.rl(51): Warning: statement is not reachable sam_alignment.rl(59): Warning: statement is not reachable sam_alignment.rl(68): Warning: statement is not reachable sam_alignment.rl(76): Warning: statement is not reachable sam_alignment.rl(82): Warning: statement is not reachable sam_alignment.rl(131): Warning: statement is not reachable sam_alignment.rl(163): Warning: statement is not reachable sam_alignment.rl(176): Warning: statement is not reachable sam_alignment.rl(188): Warning: statement is not reachable sam_alignment.rl(221): Warning: statement is not reachable sam_alignment.rl(250): Warning: statement is not reachable sam_alignment.rl(407): Warning: statement is not reachable sam_alignment.rl(52): Warning: statement is not reachable sam_alignment.rl(60): Warning: statement is not reachable sam_alignment.rl(69): Warning: statement is not reachable sam_alignment.rl(77): Warning: statement is not reachable sam_alignment.rl(83): Warning: statement is not reachable sam_alignment.rl(132): Warning: statement is not reachable sam_alignment.rl(164): Warning: statement is not reachable sam_alignment.rl(177): Warning: statement is not reachable sam_alignment.rl(189): Warning: statement is not reachable sam_alignment.rl(222): Warning: statement is not reachable sam_alignment.rl(252): Warning: statement is not reachable sam_alignment.rl(409): Warning: statement is not reachable sam_alignment.rl(51): Warning: statement is not reachable sam_alignment.rl(59): Warning: statement is not reachable sam_alignment.rl(68): Warning: statement is not reachable sam_alignment.rl(76): Warning: statement is not reachable sam_alignment.rl(82): Warning: statement is not reachable sam_alignment.rl(131): Warning: statement is not reachable sam_alignment.rl(163): Warning: statement is not reachable sam_alignment.rl(176): Warning: statement is not reachable sam_alignment.rl(188): Warning: statement is not reachable sam_alignment.rl(221): Warning: statement is not reachable sam_alignment.rl(250): Warning: statement is not reachable sam_alignment.rl(407): Warning: statement is not reachable [115/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_contrib_undead_doformat.d.o.deps -of=sambamba.p/BioD_contrib_undead_doformat.d.o -c ../BioD/contrib/undead/doformat.d ../BioD/contrib/undead/doformat.d(128): Deprecation: use of imaginary type `ifloat` is deprecated, use `float` instead ../BioD/contrib/undead/doformat.d(129): Deprecation: use of imaginary type `idouble` is deprecated, use `double` instead ../BioD/contrib/undead/doformat.d(130): Deprecation: use of imaginary type `ireal` is deprecated, use `real` instead ../BioD/contrib/undead/doformat.d(131): Deprecation: use of complex type `cfloat` is deprecated, use `std.complex.Complex!(float)` instead ../BioD/contrib/undead/doformat.d(132): Deprecation: use of complex type `cdouble` is deprecated, use `std.complex.Complex!(double)` instead ../BioD/contrib/undead/doformat.d(133): Deprecation: use of complex type `creal` is deprecated, use `std.complex.Complex!(real)` instead [116/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_maf_reader.d.o.deps -of=sambamba.p/BioD_bio_std_maf_reader.d.o -c ../BioD/bio/std/maf/reader.d [117/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_sff_reader.d.o.deps -of=sambamba.p/BioD_bio_std_sff_reader.d.o -c ../BioD/bio/std/sff/reader.d [118/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_sff_readrange.d.o.deps -of=sambamba.p/BioD_bio_std_sff_readrange.d.o -c ../BioD/bio/std/sff/readrange.d [119/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_contrib_undead_utf.d.o.deps -of=sambamba.p/BioD_contrib_undead_utf.d.o -c ../BioD/contrib/undead/utf.d [120/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_sff_writer.d.o.deps -of=sambamba.p/BioD_bio_std_sff_writer.d.o -c ../BioD/bio/std/sff/writer.d [121/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/thirdparty_mergesort.d.o.deps -of=sambamba.p/thirdparty_mergesort.d.o -c ../thirdparty/mergesort.d [122/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_contrib_undead_cstream.d.o.deps -of=sambamba.p/BioD_contrib_undead_cstream.d.o -c ../BioD/contrib/undead/cstream.d [123/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/_build_sambamba-1.0+dfsg_obj-aarch64-linux-gnu_utils_ldc_version_info_.d.o.deps -of=sambamba.p/_build_sambamba-1.0+dfsg_obj-aarch64-linux-gnu_utils_ldc_version_info_.d.o -c /build/sambamba-1.0+dfsg/obj-aarch64-linux-gnu/utils/ldc_version_info_.d [124/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/thirdparty_unstablesort.d.o.deps -of=sambamba.p/thirdparty_unstablesort.d.o -c ../thirdparty/unstablesort.d [125/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/utils_version_.d.o.deps -of=sambamba.p/utils_version_.d.o -c ../utils/version_.d [126/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/utils_strip_bcf_header.d.o.deps -of=sambamba.p/utils_strip_bcf_header.d.o -c ../utils/strip_bcf_header.d [127/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_contrib_undead_internal_file.d.o.deps -of=sambamba.p/BioD_contrib_undead_internal_file.d.o -c ../BioD/contrib/undead/internal/file.d [128/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/utils_lz4.d.o.deps -of=sambamba.p/utils_lz4.d.o -c ../utils/lz4.d [129/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_contrib_undead_stream.d.o.deps -of=sambamba.p/BioD_contrib_undead_stream.d.o -c ../BioD/contrib/undead/stream.d ../BioD/contrib/undead/stream.d(450): Deprecation: use of imaginary type `ifloat` is deprecated, use `float` instead ../BioD/contrib/undead/stream.d(451): Deprecation: use of imaginary type `idouble` is deprecated, use `double` instead ../BioD/contrib/undead/stream.d(452): Deprecation: use of imaginary type `ireal` is deprecated, use `real` instead ../BioD/contrib/undead/stream.d(453): Deprecation: use of complex type `cfloat` is deprecated, use `std.complex.Complex!(float)` instead ../BioD/contrib/undead/stream.d(454): Deprecation: use of complex type `cdouble` is deprecated, use `std.complex.Complex!(double)` instead ../BioD/contrib/undead/stream.d(455): Deprecation: use of complex type `creal` is deprecated, use `std.complex.Complex!(real)` instead ../BioD/contrib/undead/stream.d(1116): Deprecation: use of imaginary type `ifloat` is deprecated, use `float` instead ../BioD/contrib/undead/stream.d(1117): Deprecation: use of imaginary type `idouble` is deprecated, use `double` instead ../BioD/contrib/undead/stream.d(1118): Deprecation: use of imaginary type `ireal` is deprecated, use `real` instead ../BioD/contrib/undead/stream.d(1119): Deprecation: use of complex type `cfloat` is deprecated, use `std.complex.Complex!(float)` instead ../BioD/contrib/undead/stream.d(1120): Deprecation: use of complex type `cdouble` is deprecated, use `std.complex.Complex!(double)` instead ../BioD/contrib/undead/stream.d(1121): Deprecation: use of complex type `creal` is deprecated, use `std.complex.Complex!(real)` instead ../BioD/contrib/undead/doformat.d(494): Deprecation: use of complex type `creal` is deprecated, use `std.complex.Complex!(real)` instead ../BioD/contrib/undead/doformat.d(449): Deprecation: use of complex type `cfloat` is deprecated, use `std.complex.Complex!(float)` instead ../BioD/contrib/undead/doformat.d(447): Deprecation: use of complex type `cfloat` is deprecated, use `std.complex.Complex!(float)` instead ../BioD/contrib/undead/doformat.d(449): Deprecation: use of complex type `cdouble` is deprecated, use `std.complex.Complex!(double)` instead ../BioD/contrib/undead/doformat.d(447): Deprecation: use of complex type `cdouble` is deprecated, use `std.complex.Complex!(double)` instead ../BioD/contrib/undead/doformat.d(449): Deprecation: use of complex type `creal` is deprecated, use `std.complex.Complex!(real)` instead ../BioD/contrib/undead/doformat.d(447): Deprecation: use of complex type `creal` is deprecated, use `std.complex.Complex!(real)` instead ../BioD/contrib/undead/stream.d(2472): Deprecation: use of imaginary type `ifloat` is deprecated, use `float` instead ../BioD/contrib/undead/stream.d(2473): Deprecation: use of imaginary type `idouble` is deprecated, use `double` instead ../BioD/contrib/undead/stream.d(2474): Deprecation: use of imaginary type `ireal` is deprecated, use `real` instead ../BioD/contrib/undead/stream.d(2475): Deprecation: use of complex type `cfloat` is deprecated, use `std.complex.Complex!(float)` instead ../BioD/contrib/undead/stream.d(2476): Deprecation: use of complex type `cdouble` is deprecated, use `std.complex.Complex!(double)` instead ../BioD/contrib/undead/stream.d(2477): Deprecation: use of complex type `creal` is deprecated, use `std.complex.Complex!(real)` instead ../BioD/contrib/undead/stream.d(2527): Deprecation: use of imaginary type `ifloat` is deprecated, use `float` instead ../BioD/contrib/undead/stream.d(2528): Deprecation: use of imaginary type `idouble` is deprecated, use `double` instead ../BioD/contrib/undead/stream.d(2529): Deprecation: use of imaginary type `ireal` is deprecated, use `real` instead ../BioD/contrib/undead/stream.d(2530): Deprecation: use of complex type `cfloat` is deprecated, use `std.complex.Complex!(float)` instead ../BioD/contrib/undead/stream.d(2531): Deprecation: use of complex type `cdouble` is deprecated, use `std.complex.Complex!(double)` instead ../BioD/contrib/undead/stream.d(2532): Deprecation: use of complex type `creal` is deprecated, use `std.complex.Complex!(real)` instead [130/131] ldc2 -I=sambamba.p -I=. -I=.. -I../BioD -enable-color -wi -O -g -release -wi -g -release -boundscheck=off -J../ -J. -J../BioD -JBioD -makedeps=sambamba.p/BioD_bio_std_hts_utils_samheadermerger.d.o.deps -of=sambamba.p/BioD_bio_std_hts_utils_samheadermerger.d.o -c ../BioD/bio/std/hts/utils/samheadermerger.d [131/131] ldc2 -of=sambamba sambamba.p/sambamba_main.d.o sambamba.p/sambamba_depth.d.o sambamba.p/sambamba_fixbins.d.o sambamba.p/sambamba_flagstat.d.o sambamba.p/sambamba_index.d.o sambamba.p/sambamba_markdup2.d.o sambamba.p/sambamba_markdup.d.o sambamba.p/sambamba_merge.d.o sambamba.p/sambamba_pileup.d.o sambamba.p/sambamba_slice.d.o sambamba.p/sambamba_sort.d.o sambamba.p/sambamba_subsample.d.o sambamba.p/sambamba_utils_common_bed.d.o sambamba.p/sambamba_utils_common_file.d.o sambamba.p/sambamba_utils_common_filtering.d.o sambamba.p/sambamba_utils_common_intervaltree.d.o sambamba.p/sambamba_utils_common_ldc_gc_workaround.d.o sambamba.p/sambamba_utils_common_overwrite.d.o sambamba.p/sambamba_utils_common_pratt_parser.d.o sambamba.p/sambamba_utils_common_progressbar.d.o sambamba.p/sambamba_utils_common_queryparser.d.o sambamba.p/sambamba_utils_common_readstorage.d.o sambamba.p/sambamba_utils_common_tmpdir.d.o sambamba.p/sambamba_utils_view_alignmentrangeprocessor.d.o sambamba.p/sambamba_utils_view_headerserializer.d.o sambamba.p/sambamba_validate.d.o sambamba.p/sambamba_view.d.o sambamba.p/BioD_bio_core_base.d.o sambamba.p/BioD_bio_core_bgzf_block.d.o sambamba.p/BioD_bio_core_bgzf_chunk.d.o sambamba.p/BioD_bio_core_bgzf_compress.d.o sambamba.p/BioD_bio_core_bgzf_constants.d.o sambamba.p/BioD_bio_core_bgzf_inputstream.d.o sambamba.p/BioD_bio_core_bgzf_outputstream.d.o sambamba.p/BioD_bio_core_bgzf_virtualoffset.d.o sambamba.p/BioD_bio_core_call.d.o sambamba.p/BioD_bio_core_decompress.d.o sambamba.p/BioD_bio_core_genotype.d.o sambamba.p/BioD_bio_core_kmer.d.o sambamba.p/BioD_bio_core_region.d.o sambamba.p/BioD_bio_core_sequence.d.o sambamba.p/BioD_bio_core_tinymap.d.o sambamba.p/BioD_bio_core_utils_algo.d.o sambamba.p/BioD_bio_core_utils_bylinefast.d.o sambamba.p/BioD_bio_core_utils_exception.d.o sambamba.p/BioD_bio_core_utils_format.d.o sambamba.p/BioD_bio_core_utils_memoize.d.o sambamba.p/BioD_bio_core_utils_outbuffer.d.o sambamba.p/BioD_bio_core_utils_range.d.o sambamba.p/BioD_bio_core_utils_roundbuf.d.o sambamba.p/BioD_bio_core_utils_stream.d.o sambamba.p/BioD_bio_core_utils_switchendianness.d.o sambamba.p/BioD_bio_core_utils_tmpfile.d.o sambamba.p/BioD_bio_core_utils_zlib.d.o sambamba.p/BioD_bio_std_experimental_hts_bam_header.d.o sambamba.p/BioD_bio_std_experimental_hts_bam_reader.d.o sambamba.p/BioD_bio_std_experimental_hts_bam_writer.d.o sambamba.p/BioD_bio_std_experimental_hts_bgzf.d.o sambamba.p/BioD_bio_std_experimental_hts_bgzf_writer.d.o sambamba.p/BioD_bio_std_experimental_hts_constants.d.o sambamba.p/BioD_bio_std_experimental_hts_hashing.d.o sambamba.p/BioD_bio_std_experimental_hts_logger.d.o sambamba.p/BioD_bio_std_experimental_hts_pileup.d.o sambamba.p/BioD_bio_std_experimental_hts_reads.d.o sambamba.p/BioD_bio_std_experimental_hts_unpack.d.o sambamba.p/BioD_bio_std_file_fai.d.o sambamba.p/BioD_bio_std_file_fasta.d.o sambamba.p/BioD_bio_std_file_fastq.d.o sambamba.p/BioD_bio_std_genotype_maf.d.o sambamba.p/BioD_bio_std_genotype_snp.d.o sambamba.p/BioD_bio_std_hts_bam_abstractreader.d.o sambamba.p/BioD_bio_std_hts_bam_bai_bin.d.o sambamba.p/BioD_bio_std_hts_bam_baifile.d.o sambamba.p/BioD_bio_std_hts_bam_bai_indexing.d.o sambamba.p/BioD_bio_std_hts_bam_baseinfo.d.o sambamba.p/BioD_bio_std_hts_bam_cigar.d.o sambamba.p/BioD_bio_std_hts_bam_constants.d.o sambamba.p/BioD_bio_std_hts_bam_md_core.d.o sambamba.p/BioD_bio_std_hts_bam_md_operation.d.o sambamba.p/BioD_bio_std_hts_bam_md_parse.d.o sambamba.p/BioD_bio_std_hts_bam_md_reconstruct.d.o sambamba.p/BioD_bio_std_hts_bam_multireader.d.o sambamba.p/BioD_bio_std_hts_bam_pileup.d.o sambamba.p/BioD_bio_std_hts_bam_randomaccessmanager.d.o sambamba.p/BioD_bio_std_hts_bam_read.d.o sambamba.p/BioD_bio_std_hts_bam_reader.d.o sambamba.p/BioD_bio_std_hts_bam_readrange.d.o sambamba.p/BioD_bio_std_hts_bam_reference.d.o sambamba.p/BioD_bio_std_hts_bam_referenceinfo.d.o sambamba.p/BioD_bio_std_hts_bam_region.d.o sambamba.p/BioD_bio_std_hts_bam_splitter.d.o sambamba.p/BioD_bio_std_hts_bam_tagvalue.d.o sambamba.p/BioD_bio_std_hts_bam_validation_alignment.d.o sambamba.p/BioD_bio_std_hts_bam_validation_samheader.d.o sambamba.p/BioD_bio_std_hts_bam_writer.d.o sambamba.p/BioD_bio_std_hts_iontorrent_flowcall.d.o sambamba.p/BioD_bio_std_hts_iontorrent_flowindex.d.o sambamba.p/BioD_bio_std_hts_sam_header.d.o sambamba.p/BioD_bio_std_hts_sam_reader.d.o sambamba.p/BioD_bio_std_hts_sam_utils_fastrecordparser.d.o sambamba.p/BioD_bio_std_hts_sam_utils_recordparser.d.o sambamba.p/BioD_bio_std_hts_snpcallers_maq.d.o sambamba.p/BioD_bio_std_hts_snpcallers_simple.d.o sambamba.p/BioD_bio_std_hts_thirdparty_msgpack.d.o sambamba.p/BioD_bio_std_hts_utils_array.d.o sambamba.p/BioD_bio_std_hts_utils_graph.d.o sambamba.p/BioD_bio_std_hts_utils_samheadermerger.d.o sambamba.p/BioD_bio_std_hts_utils_value.d.o sambamba.p/BioD_bio_std_maf_block.d.o sambamba.p/BioD_bio_std_maf_parser.d.o sambamba.p/BioD_bio_std_maf_reader.d.o sambamba.p/BioD_bio_std_range_splitter.d.o sambamba.p/BioD_bio_std_sff_constants.d.o sambamba.p/BioD_bio_std_sff_index.d.o sambamba.p/BioD_bio_std_sff_read.d.o sambamba.p/BioD_bio_std_sff_reader.d.o sambamba.p/BioD_bio_std_sff_readrange.d.o sambamba.p/BioD_bio_std_sff_utils_roundup.d.o sambamba.p/BioD_bio_std_sff_writer.d.o sambamba.p/BioD_contrib_undead_cstream.d.o sambamba.p/BioD_contrib_undead_doformat.d.o sambamba.p/BioD_contrib_undead_internal_file.d.o sambamba.p/BioD_contrib_undead_stream.d.o sambamba.p/BioD_contrib_undead_utf.d.o sambamba.p/utils_lz4.d.o sambamba.p/utils_strip_bcf_header.d.o sambamba.p/utils_version_.d.o sambamba.p/thirdparty_mergesort.d.o sambamba.p/thirdparty_unstablesort.d.o sambamba.p/_build_sambamba-1.0+dfsg_obj-aarch64-linux-gnu_utils_ldc_version_info_.d.o -L=-flto=full -L=-rpath -L=/usr/lib/aarch64-linux-gnu -L=-rpath-link -L=/usr/lib/aarch64-linux-gnu -L=--allow-shlib-undefined -link-defaultlib-shared -L=-z -L=relro -O -g -release -wi /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/liblz4.so debian/rules override_dh_auto_test make[1]: Entering directory '/build/sambamba-1.0+dfsg' echo "FIXME: Build time tests needs fixing" FIXME: Build time tests needs fixing make[1]: Leaving directory '/build/sambamba-1.0+dfsg' create-stamp debian/debhelper-build-stamp dh_testroot -O--buildsystem=meson dh_prep -O--buildsystem=meson dh_auto_install --destdir=debian/sambamba/ -O--buildsystem=meson cd obj-aarch64-linux-gnu && DESTDIR=/build/sambamba-1.0\+dfsg/debian/sambamba LC_ALL=C.UTF-8 ninja install [0/1] Installing files. Installing sambamba to /build/sambamba-1.0+dfsg/debian/sambamba/usr/bin Installing /build/sambamba-1.0+dfsg/man/sambamba.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/man/sambamba-flagstat.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/man/sambamba-index.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/man/sambamba-markdup.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/man/sambamba-merge.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/man/sambamba-pileup.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/man/sambamba-slice.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/man/sambamba-sort.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/man/sambamba-view.1 to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/man/man1 Installing /build/sambamba-1.0+dfsg/etc/bash_completion.d/sambamba to /build/sambamba-1.0+dfsg/debian/sambamba/usr/share/bash-completion/completions dh_installdocs -O--buildsystem=meson dh_installchangelogs -O--buildsystem=meson dh_installman -O--buildsystem=meson dh_installsystemduser -O--buildsystem=meson dh_perl -O--buildsystem=meson dh_link -O--buildsystem=meson dh_strip_nondeterminism -O--buildsystem=meson dh_compress -O--buildsystem=meson dh_fixperms -O--buildsystem=meson debian/rules override_dh_missing make[1]: Entering directory '/build/sambamba-1.0+dfsg' dh_missing --fail-missing make[1]: Leaving directory '/build/sambamba-1.0+dfsg' dh_dwz -a -O--buildsystem=meson dh_strip -a -O--buildsystem=meson dh_makeshlibs -a -O--buildsystem=meson dh_shlibdeps -a -O--buildsystem=meson dh_installdeb -O--buildsystem=meson dh_gencontrol -O--buildsystem=meson dh_md5sums -O--buildsystem=meson dh_builddeb -O--buildsystem=meson dpkg-deb: building package 'sambamba' in '../sambamba_1.0+dfsg-1_arm64.deb'. dpkg-deb: building package 'sambamba-dbgsym' in '../sambamba-dbgsym_1.0+dfsg-1_arm64.deb'. dpkg-genbuildinfo --build=binary -O../sambamba_1.0+dfsg-1_arm64.buildinfo dpkg-genchanges --build=binary -O../sambamba_1.0+dfsg-1_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/11426 and its subdirectories I: Current time: Mon Apr 10 08:14:13 -12 2023 I: pbuilder-time-stamp: 1681157653 Mon Apr 10 20:14:16 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink9-arm64.debian.net. Mon Apr 10 20:14:16 UTC 2023 I: Preparing to do remote build '2' on codethink9-arm64.debian.net. Mon Apr 10 20:17:47 UTC 2023 I: Deleting $TMPDIR on codethink9-arm64.debian.net. Mon Apr 10 20:17:48 UTC 2023 I: sambamba_1.0+dfsg-1_arm64.changes: Format: 1.8 Date: Thu, 19 Jan 2023 12:18:33 +0100 Source: sambamba Binary: sambamba sambamba-dbgsym Architecture: arm64 Version: 1.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: sambamba - tools for working with SAM/BAM data Changes: sambamba (1.0+dfsg-1) unstable; urgency=medium . * Fix watch file * New upstream version * Standards-Version: 4.6.2 (routine-update) * Set field Upstream-Name in debian/copyright. * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse. Checksums-Sha1: 22f4373245bb6fc82aa2d73f20b5f8c9567a5d77 6125248 sambamba-dbgsym_1.0+dfsg-1_arm64.deb 092c4756b878c6c9c81efa77511618b0b7135742 6888 sambamba_1.0+dfsg-1_arm64.buildinfo c3a98ad390f20b65ecf90ddaa51a744cb02eab93 538428 sambamba_1.0+dfsg-1_arm64.deb Checksums-Sha256: 306290fc2a64b51754b6aa5a076eafaa121fdcd6848af53eab448a60310dc106 6125248 sambamba-dbgsym_1.0+dfsg-1_arm64.deb e03bb49efdef873b6b007a39027ba035332352af5f03e7ae3b92354c2a88ff40 6888 sambamba_1.0+dfsg-1_arm64.buildinfo 72eea1fe062168293efd2d543af77c5426536189652fb182d0a1fd07a6c7740c 538428 sambamba_1.0+dfsg-1_arm64.deb Files: d8f032602b97faa00db110a42f74fd78 6125248 debug optional sambamba-dbgsym_1.0+dfsg-1_arm64.deb 546c0f9ddd7f201c3b24fa5f49e76176 6888 science optional sambamba_1.0+dfsg-1_arm64.buildinfo 25365b713aeeae4315269a25384e0d5a 538428 science optional sambamba_1.0+dfsg-1_arm64.deb Mon Apr 10 20:17:49 UTC 2023 I: diffoscope 240 will be used to compare the two builds: # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.WvUsql4p/sambamba_1.0+dfsg-1.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.WvUsql4p/sambamba_1.0+dfsg-1.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.WvUsql4p/sambamba_1.0+dfsg-1.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.WvUsql4p/b1/sambamba_1.0+dfsg-1_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.WvUsql4p/b2/sambamba_1.0+dfsg-1_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 2.711s) 2.711s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 0.736s) 0.736s 12 calls diffoscope.comparators.binary.FilesystemFile 0.000s 10 calls abc.DotChangesFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Mon Apr 10 20:19:02 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists. Mon Apr 10 20:19:02 UTC 2023 I: sambamba from bookworm built successfully and reproducibly on arm64. Mon Apr 10 20:19:06 UTC 2023 I: Submitting .buildinfo files to external archives: Mon Apr 10 20:19:06 UTC 2023 I: Submitting 8.0K b1/sambamba_1.0+dfsg-1_arm64.buildinfo.asc Mon Apr 10 20:19:15 UTC 2023 I: Submitting 8.0K b2/sambamba_1.0+dfsg-1_arm64.buildinfo.asc Mon Apr 10 20:19:23 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Mon Apr 10 20:19:23 UTC 2023 I: Done submitting .buildinfo files. Mon Apr 10 20:19:23 UTC 2023 I: Removing signed sambamba_1.0+dfsg-1_arm64.buildinfo.asc files: removed './b1/sambamba_1.0+dfsg-1_arm64.buildinfo.asc' removed './b2/sambamba_1.0+dfsg-1_arm64.buildinfo.asc'