Input buildinfo: https://buildinfos.debian.net/buildinfo-pool/n/ngs-sdk/ngs-sdk_2.11.2-2_amd64.buildinfo Use metasnap for getting required timestamps New buildinfo file: /tmp/ngs-sdk-2.11.2-2sga3j729/ngs-sdk_2.11.2-2_amd64.buildinfo Get source package info: ngs-sdk=2.11.2-2 Source URL: http://snapshot.notset.fr/mr/package/ngs-sdk/2.11.2-2/srcfiles?fileinfo=1 env -i PATH=/usr/sbin:/usr/bin:/sbin:/bin TMPDIR=/tmp mmdebstrap --arch=amd64 --include=adduser=3.118 apt=2.3.15 autoconf=2.71-2 automake=1:1.16.5-1.1 autopoint=0.21-4 autotools-dev=20180224.1+nmu1 base-files=12.2 base-passwd=3.5.52 bash=5.1-6 binutils=2.37.90.20220130-2 binutils-common=2.37.90.20220130-2 binutils-x86-64-linux-gnu=2.37.90.20220130-2 bsdextrautils=2.37.3-1+b1 bsdutils=1:2.37.3-1+b1 build-essential=12.9 bzip2=1.0.8-5 ca-certificates=20211016 ca-certificates-java=20190909 coreutils=8.32-4.1 cpp=4:11.2.0-2 cpp-11=11.2.0-16 d-shlibs=0.104 dash=0.5.11+git20210903+057cd650a4ed-3 dctrl-tools=2.24-3+b1 debconf=1.5.79 debhelper=13.6 debian-archive-keyring=2021.1.1 debianutils=5.7-0.1 default-jdk=2:1.11-72 default-jdk-headless=2:1.11-72 default-jre=2:1.11-72 default-jre-headless=2:1.11-72 devscripts=2.22.1 dh-autoreconf=20 dh-python=5.20220119 dh-strip-nondeterminism=1.13.0-1 diffutils=1:3.7-5 dirmngr=2.2.27-3 dpkg=1.21.1 dpkg-dev=1.21.1 dwz=0.14-1 fakeroot=1.27-1 file=1:5.41-2 findutils=4.8.0-1 fontconfig-config=2.13.1-4.4 fonts-dejavu-core=2.37-2 g++=4:11.2.0-2 g++-11=11.2.0-16 gcc=4:11.2.0-2 gcc-11=11.2.0-16 gcc-11-base=11.2.0-16 gettext=0.21-4 gettext-base=0.21-4 gnupg=2.2.27-3 gnupg-l10n=2.2.27-3 gnupg-utils=2.2.27-3 gpg=2.2.27-3 gpg-agent=2.2.27-3 gpg-wks-client=2.2.27-3 gpg-wks-server=2.2.27-3 gpgconf=2.2.27-3 gpgsm=2.2.27-3 gpgv=2.2.27-3 grep=3.7-1 groff-base=1.22.4-8 gzip=1.10-4 hostname=3.23 init-system-helpers=1.61 intltool-debian=0.35.0+20060710.5 java-common=0.72 javahelper=0.78 libacl1=2.3.1-1 libapt-pkg6.0=2.3.15 libarchive-zip-perl=1.68-1 libasan6=11.2.0-16 libasound2=1.2.6.1-1 libasound2-data=1.2.6.1-1 libassuan0=2.5.5-1 libatomic1=11.2.0-16 libattr1=1:2.5.1-1 libaudit-common=1:3.0.6-1 libaudit1=1:3.0.6-1+b1 libavahi-client3=0.8-5 libavahi-common-data=0.8-5 libavahi-common3=0.8-5 libb-hooks-op-check-perl=0.22-1+b3 libbinutils=2.37.90.20220130-2 libblkid1=2.37.3-1+b1 libbrotli1=1.0.9-2+b3 libbsd0=0.11.5-1+b1 libbz2-1.0=1.0.8-5 libc-bin=2.33-5 libc-dev-bin=2.33-5 libc6=2.33-5 libc6-dev=2.33-5 libcap-ng0=0.7.9-2.2+b1 libcap2=1:2.44-1 libcc1-0=11.2.0-16 libclass-method-modifiers-perl=2.13-1 libclass-xsaccessor-perl=1.19-3+b7 libcom-err2=1.46.5-2 libcrypt-dev=1:4.4.27-1.1 libcrypt1=1:4.4.27-1.1 libctf-nobfd0=2.37.90.20220130-2 libctf0=2.37.90.20220130-2 libcups2=2.3.3op2-7 libdb5.3=5.3.28+dfsg1-0.8 libdbus-1-3=1.12.20-3 libdebconfclient0=0.261 libdebhelper-perl=13.6 libdevel-callchecker-perl=0.008-1+b2 libdpkg-perl=1.21.1 libdrm-amdgpu1=2.4.109-2 libdrm-common=2.4.109-2 libdrm-intel1=2.4.109-2 libdrm-nouveau2=2.4.109-2 libdrm-radeon1=2.4.109-2 libdrm2=2.4.109-2 libdynaloader-functions-perl=0.003-1.1 libedit2=3.1-20210910-1 libelf1=0.186-1 libencode-locale-perl=1.05-1.1 libexpat1=2.4.4-1 libfakeroot=1.27-1 libffi8=3.4.2-4 libfile-dirlist-perl=0.05-2 libfile-homedir-perl=1.006-1 libfile-listing-perl=6.14-1 libfile-stripnondeterminism-perl=1.13.0-1 libfile-touch-perl=0.12-1 libfile-which-perl=1.23-1 libfontconfig1=2.13.1-4.4 libfreetype6=2.11.1+dfsg-1 libgcc-11-dev=11.2.0-16 libgcc-s1=11.2.0-16 libgcrypt20=1.9.4-5 libgdbm-compat4=1.22-1 libgdbm6=1.22-1 libgif7=5.1.9-2 libgl1=1.4.0-1 libgl1-mesa-dri=21.3.5-1 libglapi-mesa=21.3.5-1 libglib2.0-0=2.70.3-1 libglvnd0=1.4.0-1 libglx-mesa0=21.3.5-1 libglx0=1.4.0-1 libgmp10=2:6.2.1+dfsg-3 libgnutls30=3.7.3-4+b1 libgomp1=11.2.0-16 libgpg-error0=1.43-3 libgraphite2-3=1.3.14-1 libgssapi-krb5-2=1.18.3-7 libharfbuzz0b=2.7.4-1 libhogweed6=3.7.3-1 libhtml-parser-perl=3.76-1 libhtml-tagset-perl=3.20-4 libhtml-tree-perl=5.07-2 libhttp-cookies-perl=6.10-1 libhttp-date-perl=6.05-1 libhttp-message-perl=6.36-1 libhttp-negotiate-perl=6.01-1 libicu67=67.1-7 libidn2-0=2.3.2-2 libimport-into-perl=1.002005-1 libio-html-perl=1.004-2 libio-pty-perl=1:1.15-2 libio-socket-ssl-perl=2.074-2 libipc-run-perl=20200505.0-1 libisl23=0.24-2 libitm1=11.2.0-16 libjpeg62-turbo=1:2.1.2-1 libk5crypto3=1.18.3-7 libkeyutils1=1.6.1-2 libkrb5-3=1.18.3-7 libkrb5support0=1.18.3-7 libksba8=1.6.0-2 liblcms2-2=2.12~rc1-2 libldap-2.4-2=2.4.59+dfsg-1 libllvm13=1:13.0.1~+rc3-1~exp1+b1 liblsan0=11.2.0-16 liblwp-mediatypes-perl=6.04-1 liblwp-protocol-https-perl=6.10-1 liblz4-1=1.9.3-2 liblzma5=5.2.5-2 libmagic-mgc=1:5.41-2 libmagic1=1:5.41-2 libmd0=1.0.4-1 libmodule-runtime-perl=0.016-1 libmoo-perl=2.005004-3 libmount1=2.37.3-1+b1 libmpc3=1.2.1-1 libmpdec3=2.5.1-2 libmpfr6=4.1.0-3 libncursesw6=6.3-2 libnet-http-perl=6.22-1 libnet-ssleay-perl=1.92-1 libnettle8=3.7.3-1 libnpth0=1.6-3 libnsl-dev=1.3.0-2 libnsl2=1.3.0-2 libnspr4=2:4.32-3 libnss3=2:3.73.1-1 libp11-kit0=0.24.0-6 libpam-modules=1.4.0-11 libpam-modules-bin=1.4.0-11 libpam-runtime=1.4.0-11 libpam0g=1.4.0-11 libparams-classify-perl=0.015-1+b3 libpciaccess0=0.16-3 libpcre2-8-0=10.39-3 libpcre3=2:8.39-13 libpcsclite1=1.9.5-1 libperl5.32=5.32.1-6 libpipeline1=1.5.5-1 libpng16-16=1.6.37-3 libpython3-stdlib=3.9.8-1 libpython3.10-minimal=3.10.2-1 libpython3.10-stdlib=3.10.2-1 libpython3.9-minimal=3.9.10-1 libpython3.9-stdlib=3.9.10-1 libquadmath0=11.2.0-16 libreadline8=8.1.2-1 librole-tiny-perl=2.002004-1 libsasl2-2=2.1.27+dfsg2-3 libsasl2-modules-db=2.1.27+dfsg2-3 libseccomp2=2.5.3-2 libselinux1=3.3-1+b1 libsemanage-common=3.3-1 libsemanage2=3.3-1+b1 libsensors-config=1:3.6.0-7 libsensors5=1:3.6.0-7 libsepol2=3.3-1 libsigsegv2=2.14-1 libsmartcols1=2.37.3-1+b1 libsqlite3-0=3.37.2-2 libssl1.1=1.1.1m-1 libstdc++-11-dev=11.2.0-16 libstdc++6=11.2.0-16 libsub-override-perl=0.09-2 libsub-quote-perl=2.006006-1 libsystemd0=250.3-2 libtasn1-6=4.18.0-4 libtimedate-perl=2.3300-2 libtinfo6=6.3-2 libtirpc-common=1.3.2-2 libtirpc-dev=1.3.2-2 libtirpc3=1.3.2-2 libtool=2.4.6-15 libtry-tiny-perl=0.31-1 libtsan0=11.2.0-16 libubsan1=11.2.0-16 libuchardet0=0.0.7-1 libudev1=250.3-2 libunistring2=0.9.10-6 liburi-perl=5.10-1 libuuid1=2.37.3-1+b1 libvulkan1=1.2.198.1-2 libwww-perl=6.61-1 libwww-robotrules-perl=6.02-1 libx11-6=2:1.7.2-2+b1 libx11-data=2:1.7.2-2 libx11-xcb1=2:1.7.2-2+b1 libxau6=1:1.0.9-1 libxcb-dri2-0=1.14-3 libxcb-dri3-0=1.14-3 libxcb-glx0=1.14-3 libxcb-present0=1.14-3 libxcb-shm0=1.14-3 libxcb-sync1=1.14-3 libxcb-xfixes0=1.14-3 libxcb1=1.14-3 libxdmcp6=1:1.1.2-3 libxext6=2:1.3.4-1 libxfixes3=1:6.0.0-1 libxi6=2:1.8-1 libxml2=2.9.12+dfsg-5+b1 libxrender1=1:0.9.10-1 libxshmfence1=1.3-1 libxtst6=2:1.2.3-1 libxxf86vm1=1:1.1.4-1+b2 libxxhash0=0.8.1-1 libz3-4=4.8.12-1+b1 libzstd1=1.4.8+dfsg-3 linux-libc-dev=5.15.15-2 login=1:4.11.1+dfsg1-1 lsb-base=11.1.0 m4=1.4.18-5 make=4.3-4.1 man-db=2.9.4-4 markdown=1.0.1-10.1 maven-repo-helper=1.10 mawk=1.3.4.20200120-3+b1 media-types=5.0.0 ncurses-base=6.3-2 ncurses-bin=6.3-2 netbase=6.3 openjdk-11-jdk=11.0.14+9-1 openjdk-11-jdk-headless=11.0.14+9-1 openjdk-11-jre=11.0.14+9-1 openjdk-11-jre-headless=11.0.14+9-1 openssl=1.1.1m-1 passwd=1:4.11.1+dfsg1-1 patch=2.7.6-7 patchutils=0.4.2-1 perl=5.32.1-6 perl-base=5.32.1-6 perl-modules-5.32=5.32.1-6 perl-openssl-defaults=5 pinentry-curses=1.1.0-4 po-debconf=1.0.21+nmu1 python3=3.9.8-1 python3-all=3.9.8-1 python3-distutils=3.9.10-1 python3-lib2to3=3.9.10-1 python3-minimal=3.9.8-1 python3.10=3.10.2-1 python3.10-minimal=3.10.2-1 python3.9=3.9.10-1 python3.9-minimal=3.9.10-1 readline-common=8.1.2-1 rpcsvc-proto=1.4.2-4 sed=4.8-1 sensible-utils=0.0.17 sysvinit-utils=3.01-1 tar=1.34+dfsg-1 tzdata=2021e-1 ucf=3.0043 util-linux=2.37.3-1+b1 wdiff=1.2.2-2+b1 x11-common=1:7.7+23 xz-utils=5.2.5-2 zlib1g=1:1.2.11.dfsg-2 --variant=apt --aptopt=Acquire::Check-Valid-Until "false" --aptopt=Acquire::http::Dl-Limit "1000"; --aptopt=Acquire::https::Dl-Limit "1000"; --aptopt=Acquire::Retries "5"; --aptopt=APT::Get::allow-downgrades "true"; --keyring=/usr/share/keyrings/ --essential-hook=chroot "$1" sh -c "apt-get --yes install fakeroot util-linux" --essential-hook=copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ --essential-hook=chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220208T033400Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220208T033400Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220203T152317Z/ unstable main' >> /etc/apt/sources.list && apt-get update" --customize-hook=chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash --customize-hook=chroot "$1" env sh -c "apt-get source --only-source -d ngs-sdk=2.11.2-2 && mkdir -p /build/ngs-sdk-c0c67y && dpkg-source --no-check -x /*.dsc /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2 && chown -R builduser:builduser /build/ngs-sdk-c0c67y" --customize-hook=chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1643893903" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any" --customize-hook=sync-out /build/ngs-sdk-c0c67y /tmp/ngs-sdk-2.11.2-2sga3j729 bookworm /dev/null deb http://snapshot.notset.fr/archive/debian/20220203T152317Z unstable main I: automatically chosen mode: root I: chroot architecture amd64 is equal to the host's architecture I: automatically chosen format: null I: using /tmp/mmdebstrap.4mR7rwyLy_ as tempdir I: running apt-get update... I: downloading packages with apt... I: extracting archives... I: installing essential packages... I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "apt-get --yes install fakeroot util-linux"' exec /tmp/mmdebstrap.4mR7rwyLy_ Reading package lists... Building dependency tree... util-linux is already the newest version (2.37.3-1+b1). The following NEW packages will be installed: fakeroot libfakeroot 0 upgraded, 2 newly installed, 0 to remove and 0 not upgraded. Need to get 136 kB of archives. After this operation, 406 kB of additional disk space will be used. Get:1 http://snapshot.notset.fr/archive/debian/20220203T152317Z unstable/main amd64 libfakeroot amd64 1.27-1 [48.5 kB] Get:2 http://snapshot.notset.fr/archive/debian/20220203T152317Z unstable/main amd64 fakeroot amd64 1.27-1 [87.2 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 136 kB in 0s (915 kB/s) Selecting previously unselected package libfakeroot:amd64. (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 ... 4697 files and directories currently installed.) Preparing to unpack .../libfakeroot_1.27-1_amd64.deb ... Unpacking libfakeroot:amd64 (1.27-1) ... Selecting previously unselected package fakeroot. Preparing to unpack .../fakeroot_1.27-1_amd64.deb ... Unpacking fakeroot (1.27-1) ... Setting up libfakeroot:amd64 (1.27-1) ... Setting up fakeroot (1.27-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Processing triggers for libc-bin (2.33-5) ... I: running special hook: copy-in /usr/share/keyrings/debian-archive-bullseye-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-security-automatic.gpg /usr/share/keyrings/debian-archive-bullseye-stable.gpg /usr/share/keyrings/debian-archive-buster-automatic.gpg /usr/share/keyrings/debian-archive-buster-security-automatic.gpg /usr/share/keyrings/debian-archive-buster-stable.gpg /usr/share/keyrings/debian-archive-keyring.gpg /usr/share/keyrings/debian-archive-removed-keys.gpg /usr/share/keyrings/debian-archive-stretch-automatic.gpg /usr/share/keyrings/debian-archive-stretch-security-automatic.gpg /usr/share/keyrings/debian-archive-stretch-stable.gpg /usr/share/keyrings/debian-ports-archive-keyring-removed.gpg /usr/share/keyrings/debian-ports-archive-keyring.gpg /usr/share/keyrings/debian-keyring.gpg /etc/apt/trusted.gpg.d/ I: running --essential-hook in shell: sh -c 'chroot "$1" sh -c "rm /etc/apt/sources.list && echo 'deb http://snapshot.notset.fr/archive/debian/20220208T033400Z/ bookworm main deb-src http://snapshot.notset.fr/archive/debian/20220208T033400Z/ bookworm main deb http://snapshot.notset.fr/archive/debian/20220203T152317Z/ unstable main' >> /etc/apt/sources.list && apt-get update"' exec /tmp/mmdebstrap.4mR7rwyLy_ Get:1 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm InRelease [129 kB] Hit:2 http://snapshot.notset.fr/archive/debian/20220203T152317Z unstable InRelease Ign:3 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main amd64 Packages Ign:3 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main Sources Ign:4 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main amd64 Packages Get:3 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main Sources [11.8 MB] Get:4 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main amd64 Packages [11.2 MB] Fetched 23.1 MB in 19s (1203 kB/s) Reading package lists... I: installing remaining packages inside the chroot... I: running --customize-hook in shell: sh -c 'chroot "$1" useradd --no-create-home -d /nonexistent -p "" builduser -s /bin/bash' exec /tmp/mmdebstrap.4mR7rwyLy_ I: running --customize-hook in shell: sh -c 'chroot "$1" env sh -c "apt-get source --only-source -d ngs-sdk=2.11.2-2 && mkdir -p /build/ngs-sdk-c0c67y && dpkg-source --no-check -x /*.dsc /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2 && chown -R builduser:builduser /build/ngs-sdk-c0c67y"' exec /tmp/mmdebstrap.4mR7rwyLy_ Reading package lists... NOTICE: 'ngs-sdk' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/ngs-sdk.git Please use: git clone https://salsa.debian.org/med-team/ngs-sdk.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 1115 kB of source archives. Get:1 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main ngs-sdk 2.11.2-2 (dsc) [2299 B] Get:2 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main ngs-sdk 2.11.2-2 (tar) [1101 kB] Get:3 http://snapshot.notset.fr/archive/debian/20220208T033400Z bookworm/main ngs-sdk 2.11.2-2 (diff) [12.0 kB] Fetched 1115 kB in 1s (1215 kB/s) Download complete and in download only mode W: Download is performed unsandboxed as root as file 'ngs-sdk_2.11.2-2.dsc' couldn't be accessed by user '_apt'. - pkgAcquire::Run (13: Permission denied) dpkg-source: info: extracting ngs-sdk in /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2 dpkg-source: info: unpacking ngs-sdk_2.11.2.orig.tar.gz dpkg-source: info: unpacking ngs-sdk_2.11.2-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix_jni.patch dpkg-source: info: applying do_not_exclude_certain_architectures_explicitly.patch dpkg-source: info: applying fallback-on-generic-atomic32.patch dpkg-source: info: applying enable-ppc64el.patch dpkg-source: info: applying more_archs I: running --customize-hook in shell: sh -c 'chroot "$1" env --unset=TMPDIR runuser builduser -c "cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2 && env DEB_BUILD_OPTIONS="parallel=4" LC_ALL="C.UTF-8" LC_COLLATE="C.UTF-8" SOURCE_DATE_EPOCH="1643893903" DEB_BUILD_OPTIONS=nocheck dpkg-buildpackage -uc -a amd64 --build=any"' exec /tmp/mmdebstrap.4mR7rwyLy_ dpkg-buildpackage: info: source package ngs-sdk dpkg-buildpackage: info: source version 2.11.2-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --with python3,javahelper,jh_maven_repo_helper debian/rules override_dh_auto_clean make[1]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' if [ -e ngs-sdk/Makefile.config.linux.x86_64 ] ; then \ # dh_auto_clean --sourcedirectory=ngs-sdk ; \ dh_auto_clean ; \ fi rm -rf ngs-java/x86_64-linux-gnu rm -rf ngs-bam/x86_64-linux-gnu rm -f ngs-bam/Makefile.config rm -f ngs-bam/Makefile.config.install.linux.x86_64.prl rm -f ngs-bam/Makefile.config.linux.x86_64 rm -f ngs-bam/reconfigure rm -rf ngs-sdk/ngs/unix/generic rm -rf ngs-sdk/x86_64-linux-gnu rm -rf ngs-python/build make[1]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' jh_clean mh_clean dh_clean debian/rules binary-arch dh binary-arch --with python3,javahelper,jh_maven_repo_helper dh_update_autotools_config -a dh_autoreconf -a debian/rules override_dh_auto_configure make[1]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' mkdir ngs-sdk/ngs/unix/generic && cp debian/atomic32.h ngs-sdk/ngs/unix/generic/ # # that's no standard configure script lacking support of default options \ ./configure --build=x86_64-linux-gnu --prefix=/usr -- --source=1.7 CONFIGURING ngs-sdk Configuring NGS-SDK package checking system type... Linux checking OS distributor... checking machine architecture... x86_64 checking for supported architecture... x86_64 (64 bits) is supported checking for supported OS... Linux (linux) is supported checking for supported tool chain... gcc tool chain is supported checking for gcc... gcc (Debian 11.2.0-16) 11.2.0 checking for g++... yes checking for Python 3... /usr/bin/python3 checking whether gcc accepts -Wno-array-bounds... yes checking whether g++ accepts -static-libstdc++... no configure: creating 'ld.linux.exe_cmd.sh' configure: creating 'Makefile.config.linux.x86_64' configure: creating 'Makefile.config' configure: creating 'reconfigure' build type: release build prefix: /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk build output path: /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel includedir: /usr/include bindir: /usr/bin libdir: /usr/lib sharedir: /usr/share CC = gcc -c CPP = g++ configured with: "'--build=x86_64-linux-gnu' '--prefix=/usr' '--' '--source=1.7'" CONFIGURING ngs-java Configuring NGS-JAVA package checking system type... Linux checking OS distributor... checking machine architecture... x86_64 checking for supported architecture... x86_64 (64 bits) is supported checking for supported OS... Linux (linux) is supported checking for supported tool chain... jdk tool chain is supported checking for javac... yes checking for Python 3... /usr/bin/python3 configure: creating 'Makefile.config.linux.x86_64' configure: creating 'Makefile.config' configure: creating 'reconfigure' build type: release build prefix: /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java build output path: /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java includedir: /usr/include bindir: /usr/bin libdir: /usr/lib sharedir: /usr/share javadir: /usr/jar configured with: "'--build=x86_64-linux-gnu' '--prefix=/usr' '--' '--source=1.7'" CONFIGURING ngs-python Configuring NGS-PYTHON package checking system type... Linux checking OS distributor... checking machine architecture... x86_64 checking for supported architecture... x86_64 (64 bits) is supported checking for supported OS... Linux (linux) is supported checking for supported tool chain... gcc tool chain is supported checking for gcc... gcc (Debian 11.2.0-16) 11.2.0 checking for g++... yes checking for Python 3... /usr/bin/python3 checking whether gcc accepts -Wno-array-bounds... yes checking whether g++ accepts -static-libstdc++... no checking for ngs-sdk package... configure: optional ngs-sdk package not found: skipped. checking for ncbi-vdb package... configure: optional ncbi-vdb package not found: skipped. configure: creating 'ld.linux.exe_cmd.sh' configure: creating 'Makefile.config.linux.x86_64' configure: creating 'Makefile.config' configure: creating 'reconfigure' build type: release build prefix: /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-python/x86_64-linux-gnu/ngs-python build output path: /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-python/x86_64-linux-gnu/ngs-python/linux/gcc/x86_64/rel includedir: /usr/include bindir: /usr/bin libdir: /usr/lib sharedir: /usr/share pythondir: /usr CC = gcc -c CPP = g++ configured with: "'--build=x86_64-linux-gnu' '--prefix=/usr' '--' '--source=1.7'" make[1]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' jh_linkjars -a debian/rules override_dh_auto_build make[1]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' #dh_auto_build --sourcedirectory=ngs-sdk echo "DEBPKGNAME: EBPKGNAME" DEBPKGNAME: EBPKGNAME dh_auto_build --sourcedirectory=ngs-sdk cd ngs-sdk && make -j10 make[2]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk' make[3]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch' make[3]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language' make[3]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter' make[4]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++' make[4]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java' make[4]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python' mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++ g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/ReadCollection.pic.o ReadCollection.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/ReferenceSequence.pic.o ReferenceSequence.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/ReferenceIterator.pic.o ReferenceIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/Reference.pic.o Reference.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReadCollectionItf.pic.o ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/PileupIterator.pic.o PileupIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/PileupItf.pic.o PileupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_AlignmentItf.pic.o py_AlignmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/ReadCollectionItf.pic.o ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ReadCollectionItf.pic.o jni_ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ReferenceIteratorItf.pic.o jni_ReferenceIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/Pileup.pic.o Pileup.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/PileupEventItf.pic.o PileupEventItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/PileupEventIterator.pic.o PileupEventIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/PileupEvent.pic.o PileupEvent.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/AlignmentIterator.pic.o AlignmentIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReferenceItf.pic.o ReferenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/Alignment.pic.o Alignment.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_AlignmentIteratorItf.pic.o py_AlignmentIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ReferenceItf.pic.o jni_ReferenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/ReferenceItf.pic.o ReferenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/ReadGroupIterator.pic.o ReadGroupIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/ReadGroup.pic.o ReadGroup.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReferenceSequenceItf.pic.o ReferenceSequenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/AlignmentItf.pic.o AlignmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/ReadIterator.pic.o ReadIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/Read.pic.o Read.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReadGroupItf.pic.o ReadGroupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_FragmentItf.pic.o py_FragmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/FragmentIterator.pic.o FragmentIterator.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReadItf.pic.o ReadItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/Fragment.pic.o Fragment.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/FragmentItf.pic.o FragmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/Statistics.pic.o Statistics.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/StringRef.pic.o StringRef.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++ -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ReferenceSequenceItf.pic.o jni_ReferenceSequenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_PileupIteratorItf.pic.o jni_PileupIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_PileupItf.pic.o jni_PileupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_PileupEventIteratorItf.pic.o jni_PileupEventIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_FragmentIteratorItf.pic.o py_FragmentIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/StatisticsItf.pic.o StatisticsItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PackageItf.pic.o py_PackageItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PileupEventItf.pic.o py_PileupEventItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/StringItf.pic.o StringItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o 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/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/c++/StringRef.pic.o make[4]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/c++' g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/Refcount.pic.o Refcount.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_PileupEventItf.pic.o jni_PileupEventItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ErrorMsg.pic.o ErrorMsg.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PileupItf.pic.o py_PileupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ErrBlock.pic.o ErrBlock.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_AlignmentIteratorItf.pic.o jni_AlignmentIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/ReferenceSequenceItf.pic.o ReferenceSequenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/PileupItf.pic.o PileupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/PileupEventItf.pic.o PileupEventItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_AlignmentItf.pic.o jni_AlignmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PileupIteratorItf.pic.o py_PileupIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ReadGroupIteratorItf.pic.o jni_ReadGroupIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/AlignmentItf.pic.o AlignmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/ReadGroupItf.pic.o ReadGroupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/ReadItf.pic.o ReadItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ReadGroupItf.pic.o jni_ReadGroupItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/FragmentItf.pic.o FragmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD ar rc /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-adapt-c++.a.2.11.2 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReadCollectionItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/PileupItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/PileupEventItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReferenceItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReferenceSequenceItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/AlignmentItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReadGroupItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ReadItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/FragmentItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/StatisticsItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/StringItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/Refcount.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ErrorMsg.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/adapter/ErrBlock.pic.o g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReadCollectionItf.pic.o py_ReadCollectionItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-adapt-c++.a.2 ln -s libngs-adapt-c++.a.2.11.2 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-adapt-c++.a.2 g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ReadIteratorItf.pic.o jni_ReadIteratorItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-adapt-c++.a ln -s libngs-adapt-c++.a.2 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-adapt-c++.a rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-adapt-c++-static.a ln -s libngs-adapt-c++.a /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-adapt-c++-static.a make[3]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/adapter' g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/StatisticsItf.pic.o StatisticsItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ReadItf.pic.o jni_ReadItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/PackageItf.pic.o PackageItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/StringItf.pic.o StringItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_FragmentItf.pic.o jni_FragmentItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/Refcount.pic.o Refcount.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/VTable.pic.o VTable.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/dispatch/ErrBlock.pic.o ErrBlock.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/dispatch 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-fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_String.pic.o jni_String.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_Refcount.pic.o jni_Refcount.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o 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py_ReferenceSequenceItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_StatisticsItf.pic.o py_StatisticsItf.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_Refcount.pic.o py_Refcount.cpp -fPIC -DNDEBUG -O3 -I. -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk -I/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/ngs/unix/x86_64 -MD g++ -c -std=c++11 -o 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/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_String.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_Refcount.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/java/jni_ErrorMsg.pic.o make[4]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/java' ar rc /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-bind-python.a /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_AlignmentItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_AlignmentIteratorItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_FragmentItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_FragmentIteratorItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PackageItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PileupEventItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PileupEventIteratorItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PileupItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_PileupIteratorItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReadCollectionItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReadGroupItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReadGroupIteratorItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReadItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReadIteratorItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReferenceItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReferenceIteratorItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_ReferenceSequenceItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_StatisticsItf.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_Refcount.pic.o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/language/python/py_StringItf.pic.o make[4]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language/python' make[3]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/language' make[3]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk' rm -rf /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-c++ rm -rf /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-disp rm -rf /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-java mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-disp mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-c++ rm -rf /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-python mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-java ( cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-disp; ar x /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-disp.a; ar t /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-disp.a | sed -e '/__\.SYMDEF/d' -e 's/^\(..*\)$/\/build\/ngs-sdk-c0c67y\/ngs-sdk-2.11.2\/ngs-sdk\/x86_64-linux-gnu\/ngs-sdk\/linux\/gcc\/x86_64\/rel\/obj\/ngs-disp\/\1/' > /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-disp/manifest ) ( cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-c++; ar x /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-bind-c++.a; ar t /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-bind-c++.a | sed -e '/__\.SYMDEF/d' -e 's/^\(..*\)$/\/build\/ngs-sdk-c0c67y\/ngs-sdk-2.11.2\/ngs-sdk\/x86_64-linux-gnu\/ngs-sdk\/linux\/gcc\/x86_64\/rel\/obj\/ngs-bind-c++\/\1/' > /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-c++/manifest ) mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-python ( cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-java; ar x /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-bind-java.a; ar t /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-bind-java.a | sed -e '/__\.SYMDEF/d' -e 's/^\(..*\)$/\/build\/ngs-sdk-c0c67y\/ngs-sdk-2.11.2\/ngs-sdk\/x86_64-linux-gnu\/ngs-sdk\/linux\/gcc\/x86_64\/rel\/obj\/ngs-bind-java\/\1/' > /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-java/manifest ) ( cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-python; ar x /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-bind-python.a; ar t /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib/libngs-bind-python.a | sed -e '/__\.SYMDEF/d' -e 's/^\(..*\)$/\/build\/ngs-sdk-c0c67y\/ngs-sdk-2.11.2\/ngs-sdk\/x86_64-linux-gnu\/ngs-sdk\/linux\/gcc\/x86_64\/rel\/obj\/ngs-bind-python\/\1/' > /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-python/manifest ) g++ -DNDEBUG -O3 -shared -o /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-sdk.so.2.11.2 -Wl,-soname=libngs-sdk.so.2 `cat /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-java/manifest /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-python/manifest` -L/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/ilib -lngs-disp ( ar rc /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-c++.a.2.11.2 `cat /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-bind-c++/manifest /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/obj/ngs-disp/manifest` ) rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-c++.a.2 ln -s libngs-c++.a.2.11.2 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-c++.a.2 rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-c++.a ln -s libngs-c++.a.2 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-c++.a rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-c++-static.a ln -s libngs-c++.a /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-c++-static.a rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-sdk.so.2 ln -s libngs-sdk.so.2.11.2 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-sdk.so.2 rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-sdk.so ln -s libngs-sdk.so.2 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-sdk.so make[3]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk' make[2]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk' # Remove ngs-bam generation, expects ngs-sdk and cannot find a way # to specify it #cd ngs-bam && LD_LIBRARY_PATH=../ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/*/rel/lib ./configure --build=x86_64-linux-gnu --prefix=/usr --with-ngs-sdk-prefix=../ngs-sdk #dh_auto_build --sourcedirectory=ngs-bam dh_auto_build --sourcedirectory=ngs-java -- JAVAC="javac -source 1.7 -target 1.7" cd ngs-java && make -j10 "JAVAC=javac -source 1.7 -target 1.7" make[2]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java' make[3]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java' mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar mkdir -p /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls javac -source 1.7 -target 1.7 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/ErrorMsg.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/Statistics.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/Fragment.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/FragmentIterator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/Read.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/ReadIterator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/ReadGroup.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/ReadGroupIterator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/Alignment.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/AlignmentIterator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/PileupEvent.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/PileupEventIterator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/Pileup.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/PileupIterator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/Reference.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/ReferenceIterator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/ReadCollection.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/Package.java -d /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls -classpath /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls -sourcepath /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/:/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//itf:/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/gov/nih/nlm/ncbi/ngs && touch /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls/ngs-java-api ( cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/; jar cf /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-src.jar `find gov ngs -name "*.java"`; chmod -x,o-w,g+w /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-src.jar ) || ( rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-src.jar && false ) Generating javadocs... javac -source 1.7 -target 1.7 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/examples/examples/AlignTest.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/examples/examples/AlignSliceTest.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/examples/examples/FragTest.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/examples/examples/PileupTest.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/examples/examples/RefTest.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/examples/examples/ReadGroupTest.java -d /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls -classpath /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls -sourcepath /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/:/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//itf:/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/gov/nih/nlm/ncbi/ngs && touch /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls/ngs-examples warning: [options] bootstrap class path not set in conjunction with -source 7 warning: [options] bootstrap class path not set in conjunction with -source 7 1 warning javac -source 1.7 -target 1.7 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/Refcount.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/StatisticsItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/FragmentItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/FragmentIteratorItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/ReadItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/ReadIteratorItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/ReadGroupItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/ReadGroupIteratorItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/AlignmentItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/AlignmentIteratorItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/PileupEventItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/PileupEventIteratorItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/PileupItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/PileupIteratorItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/ReferenceItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/ReferenceIteratorItf.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//ngs/itf/ReadCollectionItf.java -d /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls -classpath /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls -sourcepath /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/:/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//itf:/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/gov/nih/nlm/ncbi/ngs && touch /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls/ngs-java-itf warning: [options] bootstrap class path not set in conjunction with -source 7 Creating destination directory: "/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/javadoc/" Note: /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/ngs/itf/Refcount.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. 1 warning ( cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls; jar cf /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-examples.jar `find examples -name "*.class"`; chmod -x,o-w,g+w /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-examples.jar ) || ( rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-examples.jar && false ) Note: /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/ngs/itf/Refcount.java uses or overrides a deprecated API. Note: Recompile with -Xlint:deprecation for details. 1 warning javac -source 1.7 -target 1.7 /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/DownloadManager.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/FileCreator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/HttpManager.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/LibDependencies.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/LibManager.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/LibPathIterator.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/LibVersionChecker.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/LMProperties.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/Logger.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/Manager.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/NGS.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/Version.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/LibraryLoadError.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/LibraryNotFoundError.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/LibraryIncompatibleVersionError.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/cause/ConnectionProblemCause.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/cause/DownloadDisabledCause.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/cause/InvalidLibraryCause.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/cause/JvmErrorCause.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/cause/LibraryLoadCause.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/cause/OutdatedJarCause.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/cause/PrereleaseReqLibCause.java /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//gov/nih/nlm/ncbi/ngs/error/cause/UnsupportedArchCause.java -d /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls -classpath /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls -sourcepath /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/:/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java//itf:/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/gov/nih/nlm/ncbi/ngs && touch /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls/ngs-java-ncbi warning: [options] bootstrap class path not set in conjunction with -source 7 ( cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/javadoc ; jar cf /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-doc.jar `find . -type f`; chmod -x,o-w,g+w /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-doc.jar ) || ( rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-doc.jar && false ) 1 warning ( cd /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/cls; jar cf /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-java.jar `find . -name "*.class"`; chmod -x,o-w,g+w /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-java.jar ) || ( rm -f /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java/x86_64-linux-gnu/ngs-java/jar/ngs-java.jar && false ) make[3]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java' make[2]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-java' markdown README.md > README.html make[1]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' create-stamp debian/debhelper-build-stamp dh_prep -a debian/rules override_dh_auto_install make[1]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' d-shlibmove --commit \ --multiarch \ --devunversioned \ --exclude-a \ --exclude-la \ --movedev "ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/*/rel/lib/*.a*" usr/lib/x86_64-linux-gnu \ --movedev "ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/*/rel/ilib/*.a" usr/lib/x86_64-linux-gnu \ --movedev ngs-sdk/ngs usr/include \ ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/*/rel/lib/libngs-sdk.so Library package automatic movement utility set -e install -d -m 755 debian/libngs-sdk-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libngs-sdk2/usr/lib/x86_64-linux-gnu mv ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-sdk.so debian/libngs-sdk-dev/usr/lib/x86_64-linux-gnu mv /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-sdk.so.2 debian/libngs-sdk2/usr/lib/x86_64-linux-gnu mv /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/x86_64/rel/lib/libngs-sdk.so.2.11.2 debian/libngs-sdk2/usr/lib/x86_64-linux-gnu PKGDEV=libngs-sdk-dev PKGSHL=libngs-sdk2 install -d -m 755 debian/libngs-sdk-dev/usr/lib/x86_64-linux-gnu mv ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/*/rel/lib/*.a* debian/libngs-sdk-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libngs-sdk-dev/usr/lib/x86_64-linux-gnu mv ngs-sdk/x86_64-linux-gnu/ngs-sdk/linux/gcc/*/rel/ilib/*.a debian/libngs-sdk-dev/usr/lib/x86_64-linux-gnu install -d -m 755 debian/libngs-sdk-dev/usr/include mv ngs-sdk/ngs debian/libngs-sdk-dev/usr/include make[1]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' debian/rules override_dh_install make[1]: Entering directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' dh_install -ppython3-ngs set -e && for i in 3.10 3.9; do \ cd ngs-python ; \ python$i ./setup.py install --install-layout=deb --root ../debian/python3-ngs; \ cd .. ; \ done /build/ngs-sdk-c0c67y/ngs-sdk-2.11.2/ngs-python/./setup.py:1: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives from distutils.core import setup /usr/lib/python3.10/distutils/dist.py:274: UserWarning: Unknown distribution option: 'include_package_data' warnings.warn(msg) running install running build running build_py creating build creating build/lib creating build/lib/ngs copying ngs/Alignment.py -> build/lib/ngs copying ngs/AlignmentIterator.py -> build/lib/ngs copying ngs/ErrorMsg.py -> build/lib/ngs copying ngs/Fragment.py -> build/lib/ngs copying ngs/FragmentIterator.py -> build/lib/ngs copying ngs/LibChecker.py -> build/lib/ngs copying ngs/LibManager.py -> build/lib/ngs copying ngs/Package.py -> build/lib/ngs copying ngs/Pileup.py -> build/lib/ngs copying ngs/PileupEvent.py -> build/lib/ngs copying ngs/PileupEventIterator.py -> build/lib/ngs copying ngs/PileupIterator.py -> build/lib/ngs copying ngs/Read.py -> build/lib/ngs copying ngs/ReadCollection.py -> build/lib/ngs copying ngs/ReadGroup.py -> build/lib/ngs copying ngs/ReadGroupIterator.py -> build/lib/ngs copying ngs/ReadIterator.py -> build/lib/ngs copying ngs/Refcount.py -> build/lib/ngs copying ngs/Reference.py -> build/lib/ngs copying ngs/ReferenceIterator.py -> build/lib/ngs copying ngs/ReferenceSequence.py -> build/lib/ngs copying ngs/Statistics.py -> build/lib/ngs copying ngs/String.py -> build/lib/ngs copying ngs/__init__.py -> build/lib/ngs running install_lib creating ../debian/python3-ngs creating ../debian/python3-ngs/usr creating ../debian/python3-ngs/usr/lib creating ../debian/python3-ngs/usr/lib/python3 creating ../debian/python3-ngs/usr/lib/python3/dist-packages creating ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Alignment.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/AlignmentIterator.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ErrorMsg.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Fragment.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/FragmentIterator.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/LibChecker.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/LibManager.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Package.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Pileup.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/PileupEvent.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/PileupEventIterator.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/PileupIterator.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Read.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReadCollection.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReadGroup.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReadGroupIterator.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReadIterator.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Refcount.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Reference.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReferenceIterator.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/ReferenceSequence.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/Statistics.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/String.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs copying build/lib/ngs/__init__.py -> ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Alignment.py to Alignment.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/AlignmentIterator.py to AlignmentIterator.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ErrorMsg.py to ErrorMsg.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Fragment.py to Fragment.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/FragmentIterator.py to FragmentIterator.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/LibChecker.py to LibChecker.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/LibManager.py to LibManager.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Package.py to Package.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Pileup.py to Pileup.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupEvent.py to PileupEvent.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupEventIterator.py to PileupEventIterator.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupIterator.py to PileupIterator.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Read.py to Read.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadCollection.py to ReadCollection.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadGroup.py to ReadGroup.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadGroupIterator.py to ReadGroupIterator.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadIterator.py to ReadIterator.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Refcount.py to Refcount.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Reference.py to Reference.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReferenceIterator.py to ReferenceIterator.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReferenceSequence.py to ReferenceSequence.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Statistics.py to Statistics.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/String.py to String.cpython-310.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/__init__.py to __init__.cpython-310.pyc running install_egg_info Writing ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs-1.0.egg-info /usr/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'include_package_data' warnings.warn(msg) running install running build running build_py running install_lib byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Alignment.py to Alignment.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/AlignmentIterator.py to AlignmentIterator.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ErrorMsg.py to ErrorMsg.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Fragment.py to Fragment.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/FragmentIterator.py to FragmentIterator.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/LibChecker.py to LibChecker.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/LibManager.py to LibManager.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Package.py to Package.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Pileup.py to Pileup.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupEvent.py to PileupEvent.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupEventIterator.py to PileupEventIterator.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/PileupIterator.py to PileupIterator.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Read.py to Read.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadCollection.py to ReadCollection.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadGroup.py to ReadGroup.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadGroupIterator.py to ReadGroupIterator.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReadIterator.py to ReadIterator.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Refcount.py to Refcount.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Reference.py to Reference.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReferenceIterator.py to ReferenceIterator.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/ReferenceSequence.py to ReferenceSequence.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/Statistics.py to Statistics.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/String.py to String.cpython-39.pyc byte-compiling ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs/__init__.py to __init__.cpython-39.pyc running install_egg_info Removing ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs-1.0.egg-info Writing ../debian/python3-ngs/usr/lib/python3/dist-packages/ngs-1.0.egg-info find debian -name "*.pyc" -delete find debian -type d -name __pycache__ | xargs rm -rf make[1]: Leaving directory '/build/ngs-sdk-c0c67y/ngs-sdk-2.11.2' jh_installjavadoc -a dh_installdocs -a dh_installchangelogs -a dh_python3 -a dh_perl -a dh_link -a jh_installlibs -a jh_classpath -a jh_manifest -a jh_depends -a mh_installpoms -a mh_linkjars --skip-clean-poms -a dh_strip_nondeterminism -a dh_compress -a dh_fixperms -a dh_missing -a dh_dwz -a dwz: debian/libngs-sdk2/usr/lib/x86_64-linux-gnu/libngs-sdk.so.2.11.2: .debug_info section not present dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dh_installdeb -a dh_gencontrol -a dh_md5sums -a dh_builddeb -a dpkg-deb: building package 'libngs-sdk2' in '../libngs-sdk2_2.11.2-2_amd64.deb'. dpkg-deb: building package 'libngs-sdk2-dbgsym' in '../libngs-sdk2-dbgsym_2.11.2-2_amd64.deb'. dpkg-deb: building package 'libngs-java' in '../libngs-java_2.11.2-2_amd64.deb'. dpkg-deb: building package 'python3-ngs' in '../python3-ngs_2.11.2-2_amd64.deb'. dpkg-deb: building package 'libngs-sdk-dev' in '../libngs-sdk-dev_2.11.2-2_amd64.deb'. dpkg-genbuildinfo --build=any -O../ngs-sdk_2.11.2-2_amd64.buildinfo dpkg-genchanges --build=any -O../ngs-sdk_2.11.2-2_amd64.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) I: running special hook: sync-out /build/ngs-sdk-c0c67y /tmp/ngs-sdk-2.11.2-2sga3j729 I: cleaning package lists and apt cache... W: deleting files in /tmp: hsperfdata_root W: deleting files in /tmp: hsperfdata_builduser I: removing tempdir /tmp/mmdebstrap.4mR7rwyLy_... I: success in 650.0716 seconds md5: libngs-java_2.11.2-2_amd64.deb: OK md5: libngs-sdk-dev_2.11.2-2_amd64.deb: OK md5: libngs-sdk2-dbgsym_2.11.2-2_amd64.deb: OK md5: libngs-sdk2_2.11.2-2_amd64.deb: OK md5: python3-ngs_2.11.2-2_amd64.deb: OK sha1: libngs-java_2.11.2-2_amd64.deb: OK sha1: libngs-sdk-dev_2.11.2-2_amd64.deb: OK sha1: libngs-sdk2-dbgsym_2.11.2-2_amd64.deb: OK sha1: libngs-sdk2_2.11.2-2_amd64.deb: OK sha1: python3-ngs_2.11.2-2_amd64.deb: OK sha256: libngs-java_2.11.2-2_amd64.deb: OK sha256: libngs-sdk-dev_2.11.2-2_amd64.deb: OK sha256: libngs-sdk2-dbgsym_2.11.2-2_amd64.deb: OK sha256: libngs-sdk2_2.11.2-2_amd64.deb: OK sha256: python3-ngs_2.11.2-2_amd64.deb: OK Checksums: OK