nanopolish →
0.13.2-1 →
armhf → 2020-05-06 08:17:25
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| nanopolish 0.13.2-1 (armhf) Wed, 06 May 2020 07:35:07 +0000 |
+==============================================================================+
Package: nanopolish
Version: 0.13.2-1
Source Version: 0.13.2-1
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-64fcddb8-3fdd-453c-af58-e361775cc80b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.4 MB in 26s (952 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'nanopolish' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/nanopolish.git
Please use:
git clone https://salsa.debian.org/med-team/nanopolish.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 4077 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main nanopolish 0.13.2-1 (dsc) [2095 B]
Get:2 http://172.17.0.1/private bullseye-staging/main nanopolish 0.13.2-1 (tar) [4067 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main nanopolish 0.13.2-1 (diff) [7952 B]
Fetched 4077 kB in 0s (9031 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/nanopolish-fW0kdV/nanopolish-0.13.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/nanopolish-fW0kdV' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-FGERNj/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-FGERNj/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-FGERNj/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2619 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.2 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12225 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev
Filtered Build-Depends: debhelper-compat (= 12), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev
dpkg-deb: building package 'sbuild-build-depends-nanopolish-dummy' in '/<<BUILDDIR>>/resolver-FGERNj/apt_archive/sbuild-build-depends-nanopolish-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-nanopolish-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ Sources [552 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ Packages [633 B]
Fetched 2518 B in 1s (3242 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install nanopolish build dependencies (apt-based resolver)
----------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libbrotli1 libbsd0 libcroco3 libcurl3-gnutls
libdebhelper-perl libdeflate0 libeigen3-dev libelf1 libexpat1 libfast5-dev
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2
libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3
libicu63 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libminimap2-dev libmpdec2 libnghttp2-14 libpipeline1 libpsl5
libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librtmp1
libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libsz2 libtinfo5
libtool libuchardet0 libxml2 m4 man-db mime-support pkg-config po-debconf
python3 python3-distutils python3-lib2to3 python3-minimal python3.8
python3.8-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libeigen3-doc libmpfrc++-dev krb5-doc krb5-user libhdf5-doc liblzma-doc
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python3-doc python3-tk python3-venv
python3.8-venv python3.8-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libbrotli1 libbsd0 libcroco3 libcurl3-gnutls
libdebhelper-perl libdeflate0 libeigen3-dev libelf1 libexpat1 libfast5-dev
libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0 libgssapi-krb5-2
libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3
libicu63 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libk5crypto3
libkeyutils1 libkrb5-3 libkrb5support0 liblzma-dev libmagic-mgc libmagic1
libminimap2-dev libmpdec2 libnghttp2-14 libpipeline1 libpsl5
libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib librtmp1
libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libsz2 libtinfo5
libtool libuchardet0 libxml2 m4 man-db mime-support pkg-config po-debconf
python3 python3-distutils python3-lib2to3 python3-minimal python3.8
python3.8-minimal sbuild-build-depends-nanopolish-dummy sensible-utils
zlib1g-dev
0 upgraded, 85 newly installed, 0 to remove and 5 not upgraded.
Need to get 37.5 MB of archives.
After this operation, 127 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FGERNj/apt_archive ./ sbuild-build-depends-nanopolish-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1g-1 [1272 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.3~rc1-1 [751 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.3~rc1-1 [1627 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.2-3 [37.6 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-3 [68.1 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.3~rc1-1 [1598 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.3~rc1-1 [415 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.2-3 [20.8 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-3 [63.7 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13 [184 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.0-1 [14.8 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.2-1 [1158 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5 [592 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13 [1002 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.2-2 [78.4 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.2-2 [145 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20200315 [91.6 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf hdf5-helpers armhf 1.10.6+repack-1+rpi1 [40.0 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libaec0 armhf 1.0.4-1 [20.0 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libsz2 armhf 1.0.4-1 [6664 B]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libaec-dev armhf 1.0.4-1 [17.8 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7+rpi1 [61.5 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7+rpi1 [112 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7+rpi1 [318 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7+rpi1 [135 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1 [53.9 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.68.0-1 [284 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.5-3 [49.0 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libeigen3-dev all 3.3.7-2 [850 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103-1 armhf 1.10.6+repack-1+rpi1 [1185 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10-20200418-1+rpi1 [231 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-fortran-102 armhf 1.10.6+repack-1+rpi1 [93.3 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-100 armhf 1.10.6+repack-1+rpi1 [78.1 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.6+repack-1+rpi1 [49.7 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.6+repack-1+rpi1 [129 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.6+repack-1+rpi1 [37.0 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:1.5.2-2+b1 [110 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:1.5.2-2+b1 [179 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev all 1:1.5.2-2 [57.5 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-dev armhf 1.10.6+repack-1+rpi1 [2170 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libfast5-dev all 0.6.5-4 [49.8 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-3 [319 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-3 [4796 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libminimap2-dev armhf 2.17+dfsg-9 [119 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.30-4+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-10+rpi1 gcc-9_9.3.0-10+rpi1 libc6-dev_2.30-4+rpi1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200418-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-10+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20200315 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-10+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200418-1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-5 gcc-8-base_8.4.0-1+rpi1 gcc-9_9.3.0-10+rpi1 gcc-9-base_9.3.0-10+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hdf5-helpers_1.10.6+repack-1+rpi1 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-10+rpi1 libassuan0_2.5.3-7 libatomic1_10-20200418-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-5+rpi1 libblkid1_2.34-0.1 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4+rpi1 libc-dev-bin_2.30-4+rpi1 libc6_2.30-4+rpi1 libc6-dev_2.30-4+rpi1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200418-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdeflate0_1.5-3 libdpkg-perl_1.19.7 libeigen3-dev_3.3.7-2 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfast5-dev_0.6.5-4 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgcc-9-dev_9.3.0-10+rpi1 libgcc-s1_10-20200418-1+rpi1 libgcc1_1:10-20200418-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran5_10-20200418-1+rpi1 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200418-1+rpi1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7+rpi1 libhdf5-103-1_1.10.6+repack-1+rpi1 libhdf5-cpp-103-1_1.10.6+repack-1+rpi1 libhdf5-dev_1.10.6+repack-1+rpi1 libhdf5-fortran-102_1.10.6+repack-1+rpi1 libhdf5-hl-100_1.10.6+repack-1+rpi1 libhdf5-hl-cpp-100_1.10.6+repack-1+rpi1 libhdf5-hl-fortran-100_1.10.6+repack-1+rpi1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjpeg-dev_1:1.5.2-2 libjpeg62-turbo_1:1.5.2-2+b1 libjpeg62-turbo-dev_1:1.5.2-2+b1 libk5crypto3_1.17-7+rpi1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7+rpi1 libkrb5support0_1.17-7+rpi1 libksba8_1.3.5-2 libldap-2.4-2_2.4.49+dfsg-4+rpi1 libldap-common_2.4.49+dfsg-4+rpi1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libminimap2-dev_2.17+dfsg-9 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpsl5_0.21.0-1 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.3~rc1-1 libpython3.8-stdlib_3.8.3~rc1-1 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200418-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.5-1+rpi1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10-20200418-1+rpi1 libuchardet0_0.0.6-3 libudev1_245.5-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-3 pkg-config_0.29.2-1 po-debconf_1.0.21 python3_3.8.2-3 python3-distutils_3.8.2-2 python3-lib2to3_3.8.2-2 python3-minimal_3.8.2-3 python3.8_3.8.3~rc1-1 python3.8-minimal_3.8.3~rc1-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-nanopolish-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun May 3 17:31:53 2020 UTC
gpgv: using RSA key 84C1977A89E7EFED3E5CA62E2FD8BEDAC020EED1
gpgv: issuer "moeller@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./nanopolish_0.13.2-1.dsc
dpkg-source: info: extracting nanopolish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking nanopolish_0.13.2.orig.tar.gz
dpkg-source: info: unpacking nanopolish_0.13.2-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying add-shebang-to-script.patch
dpkg-source: info: applying reproducible.patch
dpkg-source: info: applying fix_remaining_python_interpreters.patch
dpkg-source: info: applying staticMinimap2Library.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-64fcddb8-3fdd-453c-af58-e361775cc80b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package nanopolish
dpkg-buildpackage: info: source version 0.13.2-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
sed -i~ 's/^.depend: .*/.depend:/' Makefile
touch .depend
/usr/bin/make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f nanopolish nanopolish_test src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o \
src/main/nanopolish.o src/test/nanopolish_test.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f .depend
mv Makefile~ Makefile
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch --with python3
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
dh_auto_build -a
make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f ./.depend
g++ -o src/main/nanopolish.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/main/nanopolish.cpp
g++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_extract.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend;
g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_alignment_db.cpp
g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_anchor.cpp
g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_eventalign.cpp
g++ -o src/common/fs_support.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/fs_support.cpp
g++ -o src/common/logsum.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/logsum.cpp
g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_alphabet.cpp
g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_bam_processor.cpp
g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_bam_utils.cpp
g++ -o src/common/nanopolish_common.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_common.cpp
g++ -o src/common/nanopolish_iupac.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_iupac.cpp
g++ -o src/common/nanopolish_klcs.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_klcs.cpp
g++ -o src/common/nanopolish_variant.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_variant.cpp
g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_duration_model.cpp
src/common/nanopolish_variant.cpp: In function 'void score_variant_group(VariantGroup&, Haplotype, const std::vector<HMMInputData>&, int, int, bool, uint32_t, const std::vector<std::__cxx11::basic_string<char> >&)':
src/common/nanopolish_variant.cpp:209:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
209 | fprintf(stderr, "Number of variants in span (%lu) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes!\n", num_variants);
| ~~^ ~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp
g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_transition_parameters.cpp
g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_io.cpp
g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_loader.cpp
src/io/nanopolish_fast5_io.cpp: In function 'raw_table fast5_get_raw_samples(fast5_file&, const string&, fast5_raw_scaling)':
src/io/nanopolish_fast5_io.cpp:156:28: warning: narrowing conversion of 'nsample' from 'hsize_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing]
156 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
| ^~~~~~~
src/io/nanopolish_fast5_io.cpp:156:40: warning: narrowing conversion of 'nsample' from 'hsize_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing]
156 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
| ^~~~~~~
g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_processor.cpp
g++ -o src/nanopolish_call_methylation.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_call_methylation.cpp
g++ -o src/nanopolish_call_variants.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_call_variants.cpp
g++ -o src/nanopolish_extract.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_extract.cpp
g++ -o src/nanopolish_getmodel.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_getmodel.cpp
src/nanopolish_call_methylation.cpp: In member function 'void WatchStatus::update(const string&)':
src/nanopolish_call_methylation.cpp:120:73: warning: format '%d' expects argument of type 'int', but argument 4 has type 'double' [-Wformat=]
120 | fprintf(stderr, "\33[2K\r[call-methylation] fast5 progress: %d/%d %.2lfs/fast5 [%s]", processed_fast5s, seconds_per_file, total_fast5s, message.c_str());
| ~^ ~~~~~~~~~~~~~~~~
| | |
| int double
| %f
src/nanopolish_call_methylation.cpp:120:79: warning: format '%lf' expects argument of type 'double', but argument 5 has type 'int' [-Wformat=]
120 | fprintf(stderr, "\33[2K\r[call-methylation] fast5 progress: %d/%d %.2lfs/fast5 [%s]", processed_fast5s, seconds_per_file, total_fast5s, message.c_str());
| ~~~~^ ~~~~~~~~~~~~
| | |
| double int
| %.2d
src/nanopolish_call_variants.cpp: In function 'Haplotype fix_homopolymers(const Haplotype&, const AlignmentDB&)':
src/nanopolish_call_variants.cpp:680:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
680 | fprintf(stderr, "SUM_VAR\t%zu\t%zu\t%d\t%d\t%lu\t%.5lf\t%.2lf\n", ref_hp_start, hp_length, var_sequence_length, call_window, variant_offset_end - variant_offset_start, sum_duration, log_gamma);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
g++ -o src/nanopolish_haplotype.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_haplotype.cpp
g++ -o src/nanopolish_index.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_index.cpp
src/nanopolish_haplotype.cpp: In member function 'void Haplotype::print_debug_info() const':
src/nanopolish_haplotype.cpp:172:61: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
172 | fprintf(stderr, "[haplotype-debug] ctg: %s, position: %lu\n", m_ref_name.c_str(), m_ref_position);
| ~~^ ~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
g++ -o src/nanopolish_methyltrain.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_methyltrain.cpp
g++ -o src/nanopolish_phase_reads.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_phase_reads.cpp
g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_polya_estimator.cpp
g++ -o src/nanopolish_raw_loader.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_raw_loader.cpp
src/nanopolish_polya_estimator.cpp: In function 'void estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)':
src/nanopolish_polya_estimator.cpp:765:40: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
765 | fprintf(out_fp, "%s\t%s\t%zu\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n",
| ~~^
| |
| unsigned int
| %llu
766 | read_name.c_str(), ref_name.c_str(), record->core.pos);
| ~~~~~~~~~~~~~~~~
| |
| hts_pos_t {aka long long int}
src/nanopolish_polya_estimator.cpp:823:36: warning: format '%zu' expects argument of type 'size_t', but argument 5 has type 'hts_pos_t' {aka 'long long int'} [-Wformat=]
823 | fprintf(out_fp, "%s\t%s\t%zu\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\n",
| ~~^
| |
| unsigned int
| %llu
824 | read_name.c_str(), ref_name.c_str(), record->core.pos,
| ~~~~~~~~~~~~~~~~
| |
| hts_pos_t {aka long long int}
g++ -o src/nanopolish_read_db.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_read_db.cpp
g++ -o src/nanopolish_scorereads.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_scorereads.cpp
g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_squiggle_read.cpp
g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp
g++ -o src/nanopolish_variant_db.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_variant_db.cpp
g++ -o src/nanopolish_vcf2fasta.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_vcf2fasta.cpp
g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_model_names.cpp
g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_pore_model_set.cpp
g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_poremodel.cpp
g++ -o src/training_core.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/training_core.cpp
cc -o src/thirdparty/fet.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/fet.c
cc -o src/thirdparty/scrappie/event_detection.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/scrappie/event_detection.c
cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/scrappie/scrappie_common.c
cc -o src/thirdparty/stdaln.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/stdaln.c
g++ -o nanopolish -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
g++ -o src/test/nanopolish_test.o -c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/test/nanopolish_test.cpp
g++ -o nanopolish_test -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
./nanopolish_test
===============================================================================
All tests passed (636 assertions in 6 test cases)
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
for pl in `find debian -name "*.pl"` ; do \
sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' ${pl} ; \
done
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \
sed -i '1s?^#!.*python.*?#!/usr/bin/python3?' ${pl} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_python3 -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian -name *.fast5 -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/nanopolish/usr/bin/nanopolish contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
dpkg-shlibdeps: warning: debian/nanopolish/usr/lib/nanopolish/nanopolish_test contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'nanopolish' in '../nanopolish_0.13.2-1_armhf.deb'.
dpkg-deb: building package 'nanopolish-dbgsym' in '../nanopolish-dbgsym_0.13.2-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../nanopolish_0.13.2-1_armhf.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)
--------------------------------------------------------------------------------
Build finished at 2020-05-06T08:17:14Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
nanopolish_0.13.2-1_armhf.changes:
----------------------------------
Format: 1.8
Date: Sun, 03 May 2020 19:25:27 +0200
Source: nanopolish
Binary: nanopolish nanopolish-dbgsym
Architecture: armhf
Version: 0.13.2-1
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Steffen Moeller <moeller@debian.org>
Description:
nanopolish - consensus caller for nanopore sequencing data
Changes:
nanopolish (0.13.2-1) unstable; urgency=medium
.
[ Michael R. Crusoe ]
* Team upload.
* New upstream version
* Enable building anywhere, there are no longer any SIMD intrinsics
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160ef0ceee44e0891b21dcc7d593bd92c31d2e33 6695 nanopolish_0.13.2-1_armhf.buildinfo
dfd1e7fc34d9f5e02f9376a47fd8572f7cfd5678 2287024 nanopolish_0.13.2-1_armhf.deb
Checksums-Sha256:
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430f1fd2ab0ff169158a461e8a7fbd2d40270a9c686bef179388f230d87fab97 6695 nanopolish_0.13.2-1_armhf.buildinfo
7c881e1d17c50d76e5e36539484617da9bdeedf7d2e379a26e1e817a9a36f071 2287024 nanopolish_0.13.2-1_armhf.deb
Files:
ad6701593b7ddc2871eadf7cd75f318d 8471596 debug optional nanopolish-dbgsym_0.13.2-1_armhf.deb
369b2aad073fbef444f8ad34a27a7edd 6695 science optional nanopolish_0.13.2-1_armhf.buildinfo
1c922f63c826d9a977b3191c6ab84ff5 2287024 science optional nanopolish_0.13.2-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
nanopolish-dbgsym_0.13.2-1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 8471596 bytes: control archive=652 bytes.
426 bytes, 12 lines control
302 bytes, 3 lines md5sums
Package: nanopolish-dbgsym
Source: nanopolish
Version: 0.13.2-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8809
Depends: nanopolish (= 0.13.2-1)
Section: debug
Priority: optional
Description: debug symbols for nanopolish
Build-Ids: 6c61f0bb8a3b4b7d159eba39943f18045ca6ab4b a2b9067600a96e2796cb2112e16dbfbd4add81c4
drwxr-xr-x root/root 0 2020-05-03 17:25 ./
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/debug/.build-id/6c/
-rw-r--r-- root/root 3121304 2020-05-03 17:25 ./usr/lib/debug/.build-id/6c/61f0bb8a3b4b7d159eba39943f18045ca6ab4b.debug
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/debug/.build-id/a2/
-rw-r--r-- root/root 2779528 2020-05-03 17:25 ./usr/lib/debug/.build-id/a2/b9067600a96e2796cb2112e16dbfbd4add81c4.debug
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3104440 2020-05-03 17:25 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/nanopolish.debug
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/share/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-05-03 17:25 ./usr/share/doc/nanopolish-dbgsym -> nanopolish
nanopolish_0.13.2-1_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 2287024 bytes: control archive=2120 bytes.
894 bytes, 18 lines control
2320 bytes, 30 lines md5sums
283 bytes, 12 lines * postinst #!/bin/sh
394 bytes, 12 lines * prerm #!/bin/sh
Package: nanopolish
Version: 0.13.2-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9473
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libhdf5-103-1, libhts3 (>= 1.10), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), python3:any, perl:any
Recommends: python3-biopython, python3-pysam
Suggests: perl, make
Section: science
Priority: optional
Homepage: https://github.com/jts/nanopolish
Description: consensus caller for nanopore sequencing data
Nanopolish uses a signal-level hidden Markov model for consensus calling
of nanopore genome sequencing data. It can perform signal-level analysis
of Oxford Nanopore sequencing data. Nanopolish can calculate an improved
consensus sequence for a draft genome assembly, detect base
modifications, call SNPs and indels with respect to a reference genome
and more.
drwxr-xr-x root/root 0 2020-05-03 17:25 ./
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/bin/
-rwxr-xr-x root/root 4012384 2020-05-03 17:25 ./usr/bin/nanopolish
-rwxr-xr-x root/root 75 2019-12-21 18:10 ./usr/bin/nanopolish_makerange
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/nanopolish/
-rwxr-xr-x root/root 2913 2020-05-03 17:25 ./usr/lib/nanopolish/calculate_methylation_frequency.py
-rwxr-xr-x root/root 599 2020-05-03 17:25 ./usr/lib/nanopolish/consensus-preprocess.pl
-rwxr-xr-x root/root 1044 2020-05-03 17:25 ./usr/lib/nanopolish/consensus.make
-rw-r--r-- root/root 923 2020-05-03 17:25 ./usr/lib/nanopolish/convert_all_models.py
-rw-r--r-- root/root 2738 2020-05-03 17:25 ./usr/lib/nanopolish/convert_model_to_header.py
-rw-r--r-- root/root 2090 2020-05-03 17:25 ./usr/lib/nanopolish/dropmodel.py
-rwxr-xr-x root/root 13202 2020-05-03 17:25 ./usr/lib/nanopolish/extract_reads_aligned_to_region.py
-rw-r--r-- root/root 2592 2020-05-03 17:25 ./usr/lib/nanopolish/import_ont_model.py
-rwxr-xr-x root/root 286 2020-05-03 17:25 ./usr/lib/nanopolish/import_ont_models_from_dir.sh
-rwxr-xr-x root/root 1188 2020-05-03 17:25 ./usr/lib/nanopolish/nanopolish_makerange.py
-rw-r--r-- root/root 3136 2020-05-03 17:25 ./usr/lib/nanopolish/nanopolish_merge.py
-rwxr-xr-x root/root 3725564 2020-05-03 17:25 ./usr/lib/nanopolish/nanopolish_test
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/lib/nanopolish/polya_training/
-rw-r--r-- root/root 4915 2020-05-03 17:25 ./usr/lib/nanopolish/polya_training/dump_signal.py
-rw-r--r-- root/root 2248 2020-04-23 18:43 ./usr/lib/nanopolish/polya_training/environment.yml
-rw-r--r-- root/root 4739 2020-05-03 17:25 ./usr/lib/nanopolish/polya_training/hmmplot.py
-rw-r--r-- root/root 4071 2020-05-03 17:25 ./usr/lib/nanopolish/polya_training/retrain_emission.py
-rw-r--r-- root/root 4029 2020-05-03 17:25 ./usr/lib/nanopolish/polya_training/workflow.md
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drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/share/python3/
drwxr-xr-x root/root 0 2020-05-03 17:25 ./usr/share/python3/runtime.d/
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 170576
Build-Time: 2115
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 362
Job: nanopolish_0.13.2-1
Machine Architecture: armhf
Package: nanopolish
Package-Time: 2527
Source-Version: 0.13.2-1
Space: 170576
Status: successful
Version: 0.13.2-1
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Finished at 2020-05-06T08:17:14Z
Build needed 00:42:07, 170576k disc space