Fri Apr 21 13:56:56 UTC 2023 I: starting to build filtlong/bookworm/arm64 on jenkins on '2023-04-21 13:56'
Fri Apr 21 13:56:56 UTC 2023 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_20/24440/console.log
Fri Apr 21 13:56:56 UTC 2023 I: Downloading source for bookworm/filtlong=0.2.1-3
--2023-04-21 13:56:56-- http://cdn-fastly.deb.debian.org/debian/pool/main/f/filtlong/filtlong_0.2.1-3.dsc
Connecting to 78.137.99.97:3128... connected.
Proxy request sent, awaiting response... 200 OK
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Saving to: ‘filtlong_0.2.1-3.dsc’
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2023-04-21 13:56:56 (120 MB/s) - ‘filtlong_0.2.1-3.dsc’ saved [2065/2065]
Fri Apr 21 13:56:56 UTC 2023 I: filtlong_0.2.1-3.dsc
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: filtlong
Binary: filtlong, filtlong-data
Architecture: any all
Version: 0.2.1-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/rrwick/Filtlong
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/filtlong
Vcs-Git: https://salsa.debian.org/med-team/filtlong.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), zlib1g-dev, python3-markdown, python3
Package-List:
filtlong deb science optional arch=any
filtlong-data deb science optional arch=all
Checksums-Sha1:
22c738634d0b1d08d0123ddbe019436fc40486d9 3008548 filtlong_0.2.1.orig.tar.gz
7e0fcc16e55f8eb6583389765a9dd5dc5f680a6b 6496 filtlong_0.2.1-3.debian.tar.xz
Checksums-Sha256:
e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a 3008548 filtlong_0.2.1.orig.tar.gz
895561084ebd7aeabba9fad5000b781eec7d155217855cda31adb07a95b7bb98 6496 filtlong_0.2.1-3.debian.tar.xz
Files:
d712423c2331da269bda5c56333f3097 3008548 filtlong_0.2.1.orig.tar.gz
158f49c4cc9615932c57b73db2c04837 6496 filtlong_0.2.1-3.debian.tar.xz
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Fri Apr 21 13:56:56 UTC 2023 I: Checking whether the package is not for us
Fri Apr 21 13:56:56 UTC 2023 I: Starting 1st build on remote node codethink13-arm64.debian.net.
Fri Apr 21 13:56:56 UTC 2023 I: Preparing to do remote build '1' on codethink13-arm64.debian.net.
Fri Apr 21 14:00:07 UTC 2023 I: Deleting $TMPDIR on codethink13-arm64.debian.net.
I: pbuilder: network access will be disabled during build
I: Current time: Thu May 23 08:20:00 -12 2024
I: pbuilder-time-stamp: 1716495600
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 [filtlong_0.2.1-3.dsc]
I: copying [./filtlong_0.2.1.orig.tar.gz]
I: copying [./filtlong_0.2.1-3.debian.tar.xz]
I: Extracting source
gpgv: Signature made Thu Nov 3 05:20:26 2022 -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 ./filtlong_0.2.1-3.dsc: no acceptable signature found
dpkg-source: info: extracting filtlong in filtlong-0.2.1
dpkg-source: info: unpacking filtlong_0.2.1.orig.tar.gz
dpkg-source: info: unpacking filtlong_0.2.1-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying ignore_locales_in_test_output.patch
dpkg-source: info: applying hardening.patch
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/31642/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='31642'
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.TWaFeXAd/pbuilderrc_em5R --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.TWaFeXAd/b1 --logfile b1/build.log filtlong_0.2.1-3.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 codethink13-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 22 04:50 /bin -> usr/bin
I: user script /srv/workspace/pbuilder/31642/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), zlib1g-dev, python3-markdown, python3
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 zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on python3-markdown; however:
Package python3-markdown is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 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-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libdebhelper-perl{a} libelf1{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libicu72{a} libmagic-mgc{a} libmagic1{a} libpipeline1{a} libpython3-stdlib{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libreadline8{a} libsub-override-perl{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} po-debconf{a} python3{a} python3-importlib-metadata{a} python3-markdown{a} python3-minimal{a} python3-more-itertools{a} python3-typing-extensions{a} python3-zipp{a} python3.11{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 libarchive-cpio-perl libltdl-dev libmail-sendmail-perl lynx python3-pygments python3-yaml wget
0 packages upgraded, 47 newly installed, 0 to remove and 0 not upgraded.
Need to get 24.8 MB of archives. After unpacking 101 MB will be used.
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Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 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]
Get: 22 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB]
Get: 23 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB]
Get: 24 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB]
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Get: 31 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B]
Get: 32 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get: 33 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get: 34 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB]
Get: 35 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB]
Get: 36 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB]
Get: 37 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.1+b3 [619 kB]
Get: 38 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB]
Get: 39 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get: 40 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get: 41 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB]
Get: 42 http://deb.debian.org/debian bookworm/main arm64 python3-typing-extensions all 4.4.0-1 [45.2 kB]
Get: 43 http://deb.debian.org/debian bookworm/main arm64 python3-more-itertools all 8.10.0-2 [53.0 kB]
Get: 44 http://deb.debian.org/debian bookworm/main arm64 python3-zipp all 1.0.0-6 [6696 B]
Get: 45 http://deb.debian.org/debian bookworm/main arm64 python3-importlib-metadata all 4.12.0-1 [24.9 kB]
Get: 46 http://deb.debian.org/debian bookworm/main arm64 python3-markdown all 3.4.1-2 [64.7 kB]
Get: 47 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB]
Fetched 24.8 MB in 1s (49.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
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-> Finished parsing the build-deps
I: Building the package
I: Running cd /build/filtlong-0.2.1/ && 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 > ../filtlong_0.2.1-3_source.changes
dpkg-buildpackage: info: source package filtlong
dpkg-buildpackage: info: source version 0.2.1-3
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
dh_auto_clean
make -j8 distclean
make[1]: Entering directory '/build/filtlong-0.2.1'
rm -f src/read.o src/misc.o src/main.o src/kmers.o src/arguments.o
rm -f bin/filtlong
make[1]: Leaving directory '/build/filtlong-0.2.1'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/filtlong-0.2.1'
dh_auto_build
make -j8 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/filtlong-0.2.1'
g++ -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/filtlong-0.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/read.o src/read.cpp
g++ -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/filtlong-0.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/misc.o src/misc.cpp
g++ -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/filtlong-0.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/main.o src/main.cpp
g++ -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/filtlong-0.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/kmers.o src/kmers.cpp
g++ -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/filtlong-0.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -c -o src/arguments.o src/arguments.cpp
g++ -std=c++11 -O3 -g -O2 -ffile-prefix-map=/build/filtlong-0.2.1=. -fstack-protector-strong -Wformat -Werror=format-security -o bin/filtlong src/read.o src/misc.o src/main.o src/kmers.o src/arguments.o -lz -Wl,-z,relro -Wl,-z,now
make[2]: Leaving directory '/build/filtlong-0.2.1'
markdown_py -f README.html README.md
make[1]: Leaving directory '/build/filtlong-0.2.1'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/filtlong-0.2.1'
python3 -m unittest
....................................................................
----------------------------------------------------------------------
Ran 68 tests in 118.734s
OK
find test -name __pycache__ | xargs rm -rf
make[1]: Leaving directory '/build/filtlong-0.2.1'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
dh_install
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
dh_fixperms
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 'filtlong-dbgsym' in '../filtlong-dbgsym_0.2.1-3_arm64.deb'.
dpkg-deb: building package 'filtlong' in '../filtlong_0.2.1-3_arm64.deb'.
dpkg-deb: building package 'filtlong-data' in '../filtlong-data_0.2.1-3_all.deb'.
dpkg-genbuildinfo --build=binary -O../filtlong_0.2.1-3_arm64.buildinfo
dpkg-genchanges --build=binary -O../filtlong_0.2.1-3_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/31642 and its subdirectories
I: Current time: Thu May 23 08:23:03 -12 2024
I: pbuilder-time-stamp: 1716495783
Fri Apr 21 14:00:07 UTC 2023 I: 1st build successful. Starting 2nd build on remote node codethink16-arm64.debian.net.
Fri Apr 21 14:00:07 UTC 2023 I: Preparing to do remote build '2' on codethink16-arm64.debian.net.
Fri Apr 21 14:04:30 UTC 2023 I: Deleting $TMPDIR on codethink16-arm64.debian.net.
Fri Apr 21 14:04:31 UTC 2023 I: filtlong_0.2.1-3_arm64.changes:
Format: 1.8
Date: Thu, 03 Nov 2022 18:17:41 +0100
Source: filtlong
Binary: filtlong filtlong-data filtlong-dbgsym
Architecture: all arm64
Version: 0.2.1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
filtlong - quality filtering tool for long reads of genome sequences
filtlong-data - quality filtering tool for long reads of genome sequences (testda
Changes:
filtlong (0.2.1-3) unstable; urgency=medium
.
* Fix watch file
* Standards-Version: 4.6.1 (routine-update)
Checksums-Sha1:
9bda1f4e101b497c2617db4b02521bc4f81dc394 1912980 filtlong-data_0.2.1-3_all.deb
8b87488bedd08ba85db904faac45c231b45483a6 872368 filtlong-dbgsym_0.2.1-3_arm64.deb
023ff2f70c629410817af6444d9fe582db02f63c 6029 filtlong_0.2.1-3_arm64.buildinfo
3fa45410f76976a5ec08df94a9d5eda9be2cdf8b 2929380 filtlong_0.2.1-3_arm64.deb
Checksums-Sha256:
3ae0112d2ff508d437160cd06b94e0edbe8df56b1a0a34b9fd982d037cfc63e7 1912980 filtlong-data_0.2.1-3_all.deb
49e5183f99595531cdc9b70178b8887f20fcea772f3fb01cd685f87fd59f2bd3 872368 filtlong-dbgsym_0.2.1-3_arm64.deb
549f8ff1dd40088bb01cfa17c461389ff5c71b1b89eea827d4aa8ee2c76e5304 6029 filtlong_0.2.1-3_arm64.buildinfo
b211f18b625e1896d9d82b037700ec70f47fc1b3ae220676e2d9b2c61585abb6 2929380 filtlong_0.2.1-3_arm64.deb
Files:
1d80454b2dea68ab1c9be4d765b726cd 1912980 science optional filtlong-data_0.2.1-3_all.deb
9e0a2c62bd3a1c4ee4367634445c4624 872368 debug optional filtlong-dbgsym_0.2.1-3_arm64.deb
5614c5686a123eff3b8db4af1200b136 6029 science optional filtlong_0.2.1-3_arm64.buildinfo
e0d2e3347a66402359f99bb84009e76f 2929380 science optional filtlong_0.2.1-3_arm64.deb
Fri Apr 21 14:04:32 UTC 2023 I: diffoscope 240 will be used to compare the two builds:
# Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.TWaFeXAd/filtlong_0.2.1-3.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.TWaFeXAd/filtlong_0.2.1-3.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.TWaFeXAd/filtlong_0.2.1-3.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.TWaFeXAd/b1/filtlong_0.2.1-3_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.TWaFeXAd/b2/filtlong_0.2.1-3_arm64.changes
## command (total time: 0.000s)
0.000s 1 call cmp (internal)
## has_same_content_as (total time: 0.000s)
0.000s 1 call abc.DotChangesFile
## main (total time: 0.752s)
0.752s 2 calls outputs
0.000s 1 call cleanup
## recognizes (total time: 0.084s)
0.083s 12 calls diffoscope.comparators.binary.FilesystemFile
0.000s 10 calls abc.DotChangesFile
## specialize (total time: 0.000s)
0.000s 1 call specialize
Fri Apr 21 14:04:34 UTC 2023 I: diffoscope 240 found no differences in the changes files, and a .buildinfo file also exists.
Fri Apr 21 14:04:34 UTC 2023 I: filtlong from bookworm built successfully and reproducibly on arm64.
Fri Apr 21 14:04:35 UTC 2023 I: Submitting .buildinfo files to external archives:
Fri Apr 21 14:04:35 UTC 2023 I: Submitting 8.0K b1/filtlong_0.2.1-3_arm64.buildinfo.asc
Fri Apr 21 14:04:37 UTC 2023 I: Submitting 8.0K b2/filtlong_0.2.1-3_arm64.buildinfo.asc
Fri Apr 21 14:04:38 UTC 2023 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit.
Fri Apr 21 14:04:38 UTC 2023 I: Done submitting .buildinfo files.
Fri Apr 21 14:04:38 UTC 2023 I: Removing signed filtlong_0.2.1-3_arm64.buildinfo.asc files:
removed './b1/filtlong_0.2.1-3_arm64.buildinfo.asc'
removed './b2/filtlong_0.2.1-3_arm64.buildinfo.asc'