I: pbuilder: network access will be disabled during build
I: Current time: Mon Mar 2 00:40:14 -12 2026
I: pbuilder-time-stamp: 1772455214
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-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 [twopaco_1.0.0+dfsg-1.dsc]
I: copying [./twopaco_1.0.0+dfsg.orig.tar.xz]
I: copying [./twopaco_1.0.0+dfsg-1.debian.tar.xz]
I: Extracting source
dpkg-source: warning: cannot verify inline signature for ./twopaco_1.0.0+dfsg-1.dsc: unsupported subcommand
dpkg-source: info: extracting twopaco in twopaco-1.0.0+dfsg
dpkg-source: info: unpacking twopaco_1.0.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking twopaco_1.0.0+dfsg-1.debian.tar.xz
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/1870123/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build/reproducible-path'
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=12 '
DISTRIBUTION='unstable'
HOME='/root'
HOST_ARCH='arm64'
IFS='
'
INVOCATION_ID='8c21b46c555d42479f0dc72f4eedec9f'
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='1870123'
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.WHyxFISk/pbuilderrc_3F3I --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.WHyxFISk/b1 --logfile b1/build.log twopaco_1.0.0+dfsg-1.dsc'
SUDO_GID='109'
SUDO_UID='104'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.4:3128'
I: uname -a
Linux codethink03-arm64 6.1.0-30-cloud-arm64 #1 SMP Debian 6.1.124-1 (2025-01-12) aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/1870123/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 <pbuilder-maint@lists.alioth.debian.org>
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), cmake, libtbb-dev, libtclap-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19957 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 cmake; however:
Package cmake is not installed.
pbuilder-satisfydepends-dummy depends on libtbb-dev; however:
Package libtbb-dev is not installed.
pbuilder-satisfydepends-dummy depends on libtclap-dev; however:
Package libtclap-dev 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} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libhwloc15{a} libicu72{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtbb-dev{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtclap-dev{a} libtool{a} libuchardet0{a} libunistring5{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl krb5-locales libarchive-cpio-perl libhwloc-plugins libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget
0 packages upgraded, 65 newly installed, 0 to remove and 0 not upgraded.
Need to get 41.6 MB of archives. After unpacking 164 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB]
Get: 2 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB]
Get: 3 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB]
Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3+b1 [314 kB]
Get: 5 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3+b1 [102 kB]
Get: 6 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.45-3+b1 [43.4 kB]
Get: 7 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB]
Get: 8 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB]
Get: 9 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB]
Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-1 [91.6 kB]
Get: 11 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get: 12 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB]
Get: 13 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-5 [284 kB]
Get: 14 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB]
Get: 15 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get: 16 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-2 [861 kB]
Get: 17 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB]
Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.4-2 [2267 kB]
Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu72 arm64 72.1-6 [9239 kB]
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Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1 [23.9 kB]
Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-4 [81.5 kB]
Get: 26 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B]
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Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-4 [127 kB]
Get: 29 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB]
Get: 30 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.7-2+b1 [127 kB]
Get: 31 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-8+b1 [20.3 kB]
Get: 32 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-8+b1 [55.7 kB]
Get: 33 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-1 [179 kB]
Get: 34 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB]
Get: 35 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB]
Get: 36 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.6-1 [20.9 kB]
Get: 37 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB]
Get: 38 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.19.0-3+b3 [46.9 kB]
Get: 39 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.8-2 [1363 kB]
Get: 40 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB]
Get: 41 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB]
Get: 42 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.11.1-1+b1 [324 kB]
Get: 43 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get: 44 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB]
Get: 45 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB]
Get: 46 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB]
Get: 47 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.4-2 [9898 kB]
Get: 48 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB]
Get: 49 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-2 [539 kB]
Get: 50 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get: 51 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get: 52 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-1 [19.6 kB]
Get: 53 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-1 [8584 B]
Get: 54 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get: 55 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get: 56 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB]
Get: 57 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 58 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 59 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB]
Get: 60 http://deb.debian.org/debian unstable/main arm64 libhwloc15 arm64 2.11.2-1 [141 kB]
Get: 61 http://deb.debian.org/debian unstable/main arm64 libtbbmalloc2 arm64 2022.0.0-1 [35.6 kB]
Get: 62 http://deb.debian.org/debian unstable/main arm64 libtbbbind-2-5 arm64 2022.0.0-1 [14.3 kB]
Get: 63 http://deb.debian.org/debian unstable/main arm64 libtbb12 arm64 2022.0.0-1 [66.5 kB]
Get: 64 http://deb.debian.org/debian unstable/main arm64 libtbb-dev arm64 2022.0.0-1 [199 kB]
Get: 65 http://deb.debian.org/debian unstable/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB]
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(Reading database ... 19957 files and directories currently installed.)
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I: Building the package
I: Running cd /build/reproducible-path/twopaco-1.0.0+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 > ../twopaco_1.0.0+dfsg-1_source.changes
dpkg-buildpackage: info: source package twopaco
dpkg-buildpackage: info: source version 1.0.0+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andrius Merkys <merkys@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean --sourcedir=src
dh_auto_clean -O--sourcedir=src
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dh_clean -O--sourcedir=src
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cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ../src
-- The C compiler identification is GNU 14.2.0
-- The CXX compiler identification is GNU 14.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (1.1s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_FIND_USE_PACKAGE_REGISTRY
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-- Build files have been written to: /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu
dh_auto_build -O--sourcedir=src
cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
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make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
make -f graphdump/CMakeFiles/graphdump.dir/build.make graphdump/CMakeFiles/graphdump.dir/depend
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make[3]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/twopaco-1.0.0+dfsg/src /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphdump /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphdump /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphdump/CMakeFiles/graphdump.dir/DependInfo.cmake "--color="
make[3]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/twopaco-1.0.0+dfsg/src /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor/CMakeFiles/twopaco.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
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make[3]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
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[ 7%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o
[ 21%] Building CXX object graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o
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[ 28%] Building CXX object graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o
[ 42%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o
[ 42%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o
[ 50%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphdump && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphdump/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphdump/CMakeFiles/graphdump.dir/graphdump.cpp.o -MF CMakeFiles/graphdump.dir/graphdump.cpp.o.d -o CMakeFiles/graphdump.dir/graphdump.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphdump/graphdump.cpp
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphdump && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphdump/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphdump/CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/common/streamfastaparser.cpp
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -MF CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/common/dnachar.cpp
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/constructor.cpp.o -MF CMakeFiles/twopaco.dir/constructor.cpp.o.d -o CMakeFiles/twopaco.dir/constructor.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/constructor.cpp
[ 57%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/compressedstring.cpp.o -MF CMakeFiles/twopaco.dir/compressedstring.cpp.o.d -o CMakeFiles/twopaco.dir/compressedstring.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/compressedstring.cpp
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -MF CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o.d -o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/concurrentbitvector.cpp
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphdump && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphdump/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphdump/CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -MF CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o.d -o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/common/dnachar.cpp
[ 64%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -MF CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/common/streamfastaparser.cpp
[ 71%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/test.cpp.o -MF CMakeFiles/twopaco.dir/test.cpp.o.d -o CMakeFiles/twopaco.dir/test.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/test.cpp
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -MF CMakeFiles/twopaco.dir/vertexenumerator.cpp.o.d -o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/vertexenumerator.cpp
[ 78%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -MF CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o.d -o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/common/spooky/SpookyV2.cpp
[ 85%] Building CXX object graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/c++ -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor -I/build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/../common -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -std=gnu++14 -MD -MT graphconstructor/CMakeFiles/twopaco.dir/common.cpp.o -MF CMakeFiles/twopaco.dir/common.cpp.o.d -o CMakeFiles/twopaco.dir/common.cpp.o -c /build/reproducible-path/twopaco-1.0.0+dfsg/src/graphconstructor/common.cpp
[ 92%] Linking CXX executable graphdump
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphdump && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphdump.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/graphdump.dir/link.d CMakeFiles/graphdump.dir/graphdump.cpp.o CMakeFiles/graphdump.dir/__/common/dnachar.cpp.o CMakeFiles/graphdump.dir/__/common/streamfastaparser.cpp.o -o graphdump -ltbb -lpthread
make[3]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
[ 92%] Built target graphdump
[100%] Linking CXX executable twopaco
cd /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/graphconstructor && /usr/bin/cmake -E cmake_link_script CMakeFiles/twopaco.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/twopaco-1.0.0+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,--dependency-file=CMakeFiles/twopaco.dir/link.d CMakeFiles/twopaco.dir/__/common/dnachar.cpp.o CMakeFiles/twopaco.dir/constructor.cpp.o CMakeFiles/twopaco.dir/concurrentbitvector.cpp.o CMakeFiles/twopaco.dir/compressedstring.cpp.o CMakeFiles/twopaco.dir/__/common/streamfastaparser.cpp.o CMakeFiles/twopaco.dir/test.cpp.o CMakeFiles/twopaco.dir/vertexenumerator.cpp.o CMakeFiles/twopaco.dir/__/common/spooky/SpookyV2.cpp.o CMakeFiles/twopaco.dir/common.cpp.o -o twopaco -ltbb -ltbbmalloc -ltbbmalloc_proxy -lpthread
make[3]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
[100%] Built target twopaco
make[2]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
/usr/bin/cmake -E cmake_progress_start /build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu/CMakeFiles 0
make[1]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg'
obj-*/graphconstructor/twopaco --test -f 34 example/example.fa
Test # 0 PASSED
Test # 1 PASSED
Test # 2 PASSED
Test # 3 PASSED
Test # 4 PASSED
Test # 5 PASSED
Test # 6 PASSED
Test # 7 PASSED
Test # 8 PASSED
Test # 9 PASSED
obj-*/graphconstructor/twopaco -f 20 -k 11 example/example.fa -o example/example.dbg
Threads = 1
Vertex length = 11
Hash functions = 5
Filter size = 1048576
Capacity = 1
Files:
example/example.fa
--------------------------------------------------------------------------------
Round 0, 0:1048576
Pass Filling Filtering
1 0 0
2 0 0
True junctions count = 7
False junctions count = 0
Hash table size = 7
Candidate marks count = 16
--------------------------------------------------------------------------------
Reallocating bifurcations time: 0
True marks count: 16
Edges construction time: 0
--------------------------------------------------------------------------------
Distinct junctions = 7
TwoPaCo::buildGraphMain:: allocated with scalable_malloc; freeing.
TwoPaCo::buildGraphMain:: Calling scalable_allocation_command(TBBMALLOC_CLEAN_ALL_BUFFERS, 0);
obj-*/graphdump/graphdump -f dot example/example.dbg -k 11 > example/example.dot
make[1]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -O--sourcedir=src
dh_prep -O--sourcedir=src
dh_auto_install --destdir=debian/twopaco/ -O--sourcedir=src
cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/twopaco-1.0.0\+dfsg/debian/twopaco AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
/usr/bin/cmake -S/build/reproducible-path/twopaco-1.0.0+dfsg/src -B/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "RELEASE"
-- Installing: /build/reproducible-path/twopaco-1.0.0+dfsg/debian/twopaco/usr/bin/graphdump
-- Installing: /build/reproducible-path/twopaco-1.0.0+dfsg/debian/twopaco/usr/bin/twopaco
make[1]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg/obj-aarch64-linux-gnu'
dh_installdocs -O--sourcedir=src
dh_installchangelogs -O--sourcedir=src
debian/rules override_dh_installexamples
make[1]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg'
dh_installexamples --sourcedir=/build/reproducible-path/twopaco-1.0.0+dfsg
make[1]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg'
debian/rules override_dh_installman
make[1]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg'
dh_installman --sourcedir=/build/reproducible-path/twopaco-1.0.0+dfsg
make[1]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg'
dh_installsystemduser -O--sourcedir=src
dh_perl -O--sourcedir=src
dh_link -O--sourcedir=src
dh_strip_nondeterminism -O--sourcedir=src
dh_compress -O--sourcedir=src
dh_fixperms -O--sourcedir=src
debian/rules override_dh_missing
make[1]: Entering directory '/build/reproducible-path/twopaco-1.0.0+dfsg'
dh_missing --list-missing
dh_missing: warning: CMakeLists.txt exists in src but is not installed to anywhere
dh_missing: warning: common/dnachar.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/dnachar.h exists in src but is not installed to anywhere
dh_missing: warning: common/junctionapi.h exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/Makefile exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/README.md exists in src but is not installed to anywhere (related file: "/build/reproducible-path/twopaco-1.0.0+dfsg/example/README.md")
dh_missing: warning: common/ngramhashing/characterhash.h exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/cyclichash.h exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/example.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/example2.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/example3.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/example4.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/example64bits.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/generalhash.h exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/mersennetwister.h exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/rabinkarphash.h exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/speedtesting.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/threewisehash.h exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/unit.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/ngramhashing/ztimer.h exists in src but is not installed to anywhere
dh_missing: warning: common/spooky/SpookyV2.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/spooky/SpookyV2.h exists in src but is not installed to anywhere
dh_missing: warning: common/streamfastaparser.cpp exists in src but is not installed to anywhere
dh_missing: warning: common/streamfastaparser.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/CMakeLists.txt exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/assemblyedgeconstructor.cpp exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/assemblyedgeconstructor.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/bifurcationstorage.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/candidateoccurence.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/common.cpp exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/common.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/compressedstring.cpp exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/compressedstring.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/concurrentbitvector.cpp exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/concurrentbitvector.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/constructor.cpp exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/test.cpp exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/test.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/vertexenumerator.cpp exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/vertexenumerator.h exists in src but is not installed to anywhere
dh_missing: warning: graphconstructor/vertexrollinghash.h exists in src but is not installed to anywhere
dh_missing: warning: graphdump/CMakeLists.txt exists in src but is not installed to anywhere
dh_missing: warning: graphdump/glueGfa1.py exists in src but is not installed to anywhere
dh_missing: warning: graphdump/glueGfa2.py exists in src but is not installed to anywhere
dh_missing: warning: graphdump/graphdump.cpp exists in src but is not installed to anywhere
dh_missing: warning: naiveconstructor/naiveconstructor.cpp exists in src but is not installed to anywhere
While detecting missing files, dh_missing noted some files with a similar name to those
that were missing. This warning /might/ be resolved by replacing references to the
missing files with the similarly named ones that dh_missing found - assuming the content
is identical.
As an example, you might want to replace:
* /build/reproducible-path/twopaco-1.0.0+dfsg/example/README.md
with:
* common/ngramhashing/README.md
in a file in debian/ or as argument to one of the dh_* tools called from debian/rules.
(Note it is possible the paths are not used verbatim but instead directories
containing or globs matching them are used instead)
Alternatively, add the missing file to debian/not-installed if it cannot and should not
be used.
The following debhelper tools have reported what they installed (with files per package)
* dh_installdocs: twopaco (0)
* dh_installexamples: twopaco (10)
* dh_installman: twopaco (2)
If the missing files are installed by another tool, please file a bug against it.
When filing the report, if the tool is not part of debhelper itself, please reference the
"Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+).
(in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.md.gz)
Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built
If the omission is intentional or no other helper can take care of this consider adding the
paths to debian/not-installed.
make[1]: Leaving directory '/build/reproducible-path/twopaco-1.0.0+dfsg'
dh_dwz -a -O--sourcedir=src
dh_strip -a -O--sourcedir=src
dh_makeshlibs -a -O--sourcedir=src
dh_shlibdeps -a -O--sourcedir=src
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 from: /lib/ld-linux-aarch64.so.1
dpkg-shlibdeps: warning: diversions involved - output may be incorrect
diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged
dh_installdeb -O--sourcedir=src
dh_gencontrol -O--sourcedir=src
dh_md5sums -O--sourcedir=src
dh_builddeb -O--sourcedir=src
dpkg-deb: building package 'twopaco' in '../twopaco_1.0.0+dfsg-1_arm64.deb'.
dpkg-deb: building package 'twopaco-dbgsym' in '../twopaco-dbgsym_1.0.0+dfsg-1_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../twopaco_1.0.0+dfsg-1_arm64.buildinfo
dpkg-genchanges --build=binary -O../twopaco_1.0.0+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/1870123 and its subdirectories
I: Current time: Mon Mar 2 00:42:26 -12 2026
I: pbuilder-time-stamp: 1772455346