I: pbuilder: network access will be disabled during build
I: Current time: Tue May 28 09:26:36 -12 2024
I: pbuilder-time-stamp: 1716931596
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
I: copying local configuration
W: --override-config is not set; not updating apt.conf Read the manpage for details.
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [uc-echo_1.12-18.dsc]
I: copying [./uc-echo_1.12.orig.tar.gz]
I: copying [./uc-echo_1.12-18.debian.tar.xz]
I: Extracting source
gpgv: Signature made Sat Feb 4 19:49:35 2023 -12
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./uc-echo_1.12-18.dsc: no acceptable signature found
dpkg-source: info: extracting uc-echo in uc-echo-1.12
dpkg-source: info: unpacking uc-echo_1.12.orig.tar.gz
dpkg-source: info: unpacking uc-echo_1.12-18.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening-flags.patch
dpkg-source: info: applying include.patch
dpkg-source: info: applying m64-flag.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying using_int_not_char.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/26033/tmp/hooks/D02_print_environment starting
I: set
BUILDDIR='/build'
BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
BUILDUSERNAME='pbuilder1'
BUILD_ARCH='arm64'
DEBIAN_FRONTEND='noninteractive'
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8'
DISTRIBUTION='bookworm'
HOME='/var/lib/jenkins'
HOST_ARCH='arm64'
IFS='
'
LANG='C'
LANGUAGE='en_US:en'
LC_ALL='C'
MAIL='/var/mail/root'
OPTIND='1'
PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
PBCURRENTCOMMANDLINEOPERATION='build'
PBUILDER_OPERATION='build'
PBUILDER_PKGDATADIR='/usr/share/pbuilder'
PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
PBUILDER_SYSCONFDIR='/etc'
PPID='26033'
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.Dv7PBkmE/pbuilderrc_h2Ua --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.Dv7PBkmE/b1 --logfile b1/build.log uc-echo_1.12-18.dsc'
SUDO_GID='117'
SUDO_UID='110'
SUDO_USER='jenkins'
TERM='unknown'
TZ='/usr/share/zoneinfo/Etc/GMT+12'
USER='root'
USERNAME='root'
_='/usr/bin/systemd-run'
http_proxy='http://192.168.101.16:3128'
I: uname -a
Linux codethink15-arm64 4.15.0-209-generic #220-Ubuntu SMP Tue Mar 21 19:52:44 UTC 2023 aarch64 GNU/Linux
I: ls -l /bin
lrwxrwxrwx 1 root root 7 May 24 04:47 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/26033/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), dh-python, python3:any, python3-scipy, python3-numpy
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19616 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on python3:any.
pbuilder-satisfydepends-dummy depends on python3-scipy; however:
Package python3-scipy is not installed.
pbuilder-satisfydepends-dummy depends on python3-numpy; however:
Package python3-numpy is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libboost-dev{a} libboost1.74-dev{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libicu72{a} libjs-jquery{a} libjs-sphinxdoc{a} libjs-underscore{a} liblapack3{a} liblbfgsb0{a} libmagic-mgc{a} libmagic1{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libpipeline1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} libxsimd-dev{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-all{a} python3-all-dev{a} python3-beniget{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-gast{a} python3-lib2to3{a} python3-minimal{a} python3-numpy{a} python3-pkg-resources{a} python3-ply{a} python3-pythran{a} python3-scipy{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl javascript-common libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pil wget
0 packages upgraded, 76 newly installed, 0 to remove and 0 not upgraded.
Need to get 71.8 MB of archives. After unpacking 446 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB]
Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB]
Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB]
Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB]
Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB]
Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB]
Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB]
Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB]
Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB]
Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B]
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Get: 12 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB]
Get: 13 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB]
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Get: 19 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB]
Get: 20 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB]
Get: 21 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB]
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Get: 39 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
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Get: 44 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB]
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Get: 49 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB]
Get: 50 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB]
Get: 51 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB]
Get: 52 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB]
Get: 53 http://deb.debian.org/debian bookworm/main arm64 libopenblas0-pthread arm64 0.3.21+ds-4 [4532 kB]
Get: 54 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB]
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Get: 59 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB]
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Get: 63 http://deb.debian.org/debian bookworm/main arm64 libpython3-all-dev arm64 3.11.2-1+b1 [1068 B]
Get: 64 http://deb.debian.org/debian bookworm/main arm64 libxsimd-dev arm64 8.1.0-7 [88.8 kB]
Get: 65 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1+b1 [1064 B]
Get: 66 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB]
Get: 67 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB]
Get: 68 http://deb.debian.org/debian bookworm/main arm64 python3-all-dev arm64 3.11.2-1+b1 [1076 B]
Get: 69 http://deb.debian.org/debian bookworm/main arm64 python3-gast all 0.5.2-2 [9364 B]
Get: 70 http://deb.debian.org/debian bookworm/main arm64 python3-beniget all 0.4.1-3 [9920 B]
Get: 71 http://deb.debian.org/debian bookworm/main arm64 python3-decorator all 5.1.1-3 [14.9 kB]
Get: 72 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB]
Get: 73 http://deb.debian.org/debian bookworm/main arm64 python3-numpy arm64 1:1.24.2-1 [4751 kB]
Get: 74 http://deb.debian.org/debian bookworm/main arm64 python3-ply all 3.11-5 [65.8 kB]
Get: 75 http://deb.debian.org/debian bookworm/main arm64 python3-pythran arm64 0.11.0+ds-7 [427 kB]
Get: 76 http://deb.debian.org/debian bookworm/main arm64 python3-scipy arm64 1.10.1-2 [14.2 MB]
Fetched 71.8 MB in 1s (53.1 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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I: Building the package
I: Running cd /build/uc-echo-1.12/ && 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 > ../uc-echo_1.12-18_source.changes
dpkg-buildpackage: info: source package uc-echo
dpkg-buildpackage: info: source version 1.12-18
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
debian/rules clean
dh clean --with python3
dh_auto_clean
make -j8 clean
make[1]: Entering directory '/build/uc-echo-1.12'
rm -f DNASeq.o NeighborSet.o KmerHashMap.o hashing NeighborJoin NeighborJoinParam NeighborMerge Voting HashMerge
make[1]: Leaving directory '/build/uc-echo-1.12'
dh_clean
debian/rules binary
dh binary --with python3
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make[1]: Entering directory '/build/uc-echo-1.12'
echo "I: DEB_HOST_ARCH: arm64"
I: DEB_HOST_ARCH: arm64
echo "I: ADDCXXFLAGS: "
I: ADDCXXFLAGS:
echo "I: CXXFLAGS: -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security "
I: CXXFLAGS: -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security
dh_auto_build
make -j8 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/uc-echo-1.12'
g++ -c -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 DNASeq.cpp -o DNASeq.o
g++ -c -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 NeighborSet.cpp -o NeighborSet.o
g++ -c -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 KmerHashMap.cpp -o KmerHashMap.o
g++ -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o hashing hashing.cpp DNASeq.o NeighborSet.o KmerHashMap.o
g++ -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o NeighborJoin NeighborJoin.cpp DNASeq.o NeighborSet.o KmerHashMap.o
g++ -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o NeighborJoinParam NeighborJoinParam.cpp DNASeq.o NeighborSet.o KmerHashMap.o
g++ -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o NeighborMerge NeighborMerge.cpp DNASeq.o NeighborSet.o KmerHashMap.o
g++ -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o Voting Voting.cpp DNASeq.o NeighborSet.o KmerHashMap.o
g++ -g -O2 -ffile-prefix-map=/build/uc-echo-1.12=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O3 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o HashMerge HashMerge.cpp DNASeq.o NeighborSet.o KmerHashMap.o
In file included from NeighborMerge.cpp:16:
NeighborSet.hpp: In member function 'void NeighborSetLoader::load(unsigned int, unsigned int)':
NeighborSet.hpp:163:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
163 | fread(&numNeighbors, sizeof(unsigned int), 1, NeighborFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NeighborSet.hpp:169:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
169 | fread(&neighborId, sizeof(unsigned int), 1, NeighborFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NeighborSet.hpp:171:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
171 | fread(&offset, sizeof(NeighborInfo::index_t), 1, NeighborFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NeighborSet.hpp:173:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
173 | fread(&nerr, sizeof(NeighborInfo::index_t), 1, NeighborFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from Voting.cpp:19:
NeighborSet.hpp: In member function 'void NeighborSetLoader::load(unsigned int, unsigned int)':
NeighborSet.hpp:163:18: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
163 | fread(&numNeighbors, sizeof(unsigned int), 1, NeighborFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NeighborSet.hpp:169:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
169 | fread(&neighborId, sizeof(unsigned int), 1, NeighborFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NeighborSet.hpp:171:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
171 | fread(&offset, sizeof(NeighborInfo::index_t), 1, NeighborFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
NeighborSet.hpp:173:22: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
173 | fread(&nerr, sizeof(NeighborInfo::index_t), 1, NeighborFile);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[2]: Leaving directory '/build/uc-echo-1.12'
make[1]: Leaving directory '/build/uc-echo-1.12'
dh_auto_test
create-stamp debian/debhelper-build-stamp
dh_prep
debian/rules override_dh_auto_install
make[1]: Entering directory '/build/uc-echo-1.12'
dh_auto_install
dh_installchangelogs README
make[1]: Leaving directory '/build/uc-echo-1.12'
dh_install
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dh_installman
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dh_lintian
dh_perl
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dh_compress
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/uc-echo-1.12'
dh_fixperms
chmod +x debian/*/usr/lib/*/*.py
make[1]: Leaving directory '/build/uc-echo-1.12'
dh_missing
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
dpkg-deb: building package 'uc-echo-dbgsym' in '../uc-echo-dbgsym_1.12-18_arm64.deb'.
dpkg-deb: building package 'uc-echo' in '../uc-echo_1.12-18_arm64.deb'.
dpkg-genbuildinfo --build=binary -O../uc-echo_1.12-18_arm64.buildinfo
dpkg-genchanges --build=binary -O../uc-echo_1.12-18_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: not including original 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/26033 and its subdirectories
I: Current time: Tue May 28 09:29:07 -12 2024
I: pbuilder-time-stamp: 1716931747