nanopolish →
0.14.0-1 →
armhf → 2022-07-17 05:52:20
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| nanopolish 0.14.0-1 (armhf) Sun, 17 Jul 2022 05:41:54 +0000 |
+==============================================================================+
Package: nanopolish
Version: 0.14.0-1
Source Version: 0.14.0-1
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-78679256-3881-46b8-99af-072096909e77' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.1 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.0 MB]
Fetched 27.2 MB in 12s (2356 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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 4085 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main nanopolish 0.14.0-1 (dsc) [2114 B]
Get:2 http://172.17.4.1/private bookworm-staging/main nanopolish 0.14.0-1 (tar) [4074 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main nanopolish 0.14.0-1 (diff) [8976 B]
Fetched 4085 kB in 1s (6807 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/nanopolish-0mj9Ge/nanopolish-0.14.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/nanopolish-0mj9Ge' 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-kkCthI/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-kkCthI/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-kkCthI/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-kkCthI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (3168 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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 48 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-kkCthI/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 (56.7 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12794 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 (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev
dpkg-deb: building package 'sbuild-build-depends-nanopolish-dummy' in '/<<BUILDDIR>>/resolver-kkCthI/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-kkCthI/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ Sources [555 B]
Get:5 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ Packages [636 B]
Fetched 2524 B in 0s (5111 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 packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils 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 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
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
libhtscodecs2 libicu71 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
liblzma-dev libmagic-mgc libmagic1 libminimap2-dev libmpdec3 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librtmp1 libsigsegv2 libslow5-0 libslow5-dev libssh2-1
libssl-dev libssl3 libstreamvbyte-dev libstreamvbyte0 libsub-override-perl
libsz2 libtool libuchardet0 libxml2 m4 man-db media-types pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3.10 python3.10-minimal zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev
groff libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev libeigen3-doc libmpfrc++-dev libhdf5-doc
liblzma-doc libssl-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser libmail-box-perl python3-doc python3-tk
python3-venv python3.10-venv python3.10-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils 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 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
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
libhtscodecs2 libicu71 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev
liblzma-dev libmagic-mgc libmagic1 libminimap2-dev libmpdec3 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.10-minimal
libpython3.10-stdlib librtmp1 libsigsegv2 libslow5-0 libslow5-dev libssh2-1
libssl-dev libstreamvbyte-dev libstreamvbyte0 libsub-override-perl libsz2
libtool libuchardet0 libxml2 m4 man-db media-types pkg-config po-debconf
python3 python3-distutils python3-lib2to3 python3-minimal python3.10
python3.10-minimal sbuild-build-depends-nanopolish-dummy zlib1g-dev
The following packages will be upgraded:
libssl3
1 upgraded, 84 newly installed, 0 to remove and 47 not upgraded.
Need to get 41.0 MB of archives.
After this operation, 140 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-kkCthI/apt_archive ./ sbuild-build-depends-nanopolish-dummy 0.invalid.0 [924 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libssl3 armhf 3.0.4-2 [1643 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.5-1+b1 [815 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.8-1 [84.1 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.5-1+b1 [1637 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.4-1+b1 [38.9 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.5-1+b1 [1626 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.5-1+b1 [542 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.4-1+b1 [21.9 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.4-1+b1 [38.4 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38-4 [137 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-1 [33.7 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-1 [1362 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-6 [171 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-6 [510 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.8 [195 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-1 [175 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-6 [1214 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.8 [1070 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.12-1 [79.9 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.9.12-1 [146 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220403 [113 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf hdf5-helpers armhf 1.10.7+repack-4+rpi1+b1 [43.2 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libaec0 armhf 1.0.6-1 [19.3 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf libsz2 armhf 1.0.6-1 [7452 B]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libaec-dev armhf 1.0.6-1 [17.6 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.47.0-1+b1 [65.3 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.83.1-2 [313 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.83.1-2 [317 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.83.1-2 [389 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.12-1 [60.5 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.12-1 [51.8 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.72.3-1 [1233 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libeigen3-dev all 3.4.0-3 [1040 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-103-1 armhf 1.10.7+repack-4+rpi1+b1 [1240 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 12.1.0-2+rpi1 [238 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-fortran-102 armhf 1.10.7+repack-4+rpi1+b1 [97.4 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-100 armhf 1.10.7+repack-4+rpi1+b1 [82.4 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.7+repack-4+rpi1+b1 [54.2 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.7+repack-4+rpi1+b1 [132 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.7+repack-4+rpi1+b1 [40.3 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4+b2 [183 kB]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo armhf 1:2.1.2-1 [144 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.2-1 [261 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libjpeg-dev armhf 1:2.1.2-1 [74.7 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libssl-dev armhf 3.0.4-2 [2123 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libhdf5-dev armhf 1.10.7+repack-4+rpi1+b1 [2208 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libfast5-dev all 0.6.5-7 [50.2 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.2.2-1 [53.1 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2+b1 [339 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2+b1 [4045 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libminimap2-dev armhf 2.24+dfsg-2 [121 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libslow5-0 armhf 0.5.1+dfsg-2 [53.6 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libslow5-dev armhf 0.5.1+dfsg-2 [64.7 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libstreamvbyte0 armhf 0.4.1-4 [5120 B]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libstreamvbyte-dev armhf 0.4.1-4 [6032 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 41.0 MB in 6s (6543 kB/s)
(Reading database ... 12794 files and directories currently installed.)
Preparing to unpack .../libssl3_3.0.4-2_armhf.deb ...
Unpacking libssl3:armhf (3.0.4-2) over (3.0.3-8) ...
Selecting previously unselected package libpython3.10-minimal:armhf.
Preparing to unpack .../libpython3.10-minimal_3.10.5-1+b1_armhf.deb ...
Unpacking libpython3.10-minimal:armhf (3.10.5-1+b1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../libexpat1_2.4.8-1_armhf.deb ...
Unpacking libexpat1:armhf (2.4.8-1) ...
Selecting previously unselected package python3.10-minimal.
Preparing to unpack .../python3.10-minimal_3.10.5-1+b1_armhf.deb ...
Unpacking python3.10-minimal (3.10.5-1+b1) ...
Setting up libssl3:armhf (3.0.4-2) ...
Setting up libpython3.10-minimal:armhf (3.10.5-1+b1) ...
Setting up libexpat1:armhf (2.4.8-1) ...
Setting up python3.10-minimal (3.10.5-1+b1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13099 files and directories currently installed.)
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5-serial.pc to provide /usr/lib/arm-linux-gnueabihf/pkgconfig/hdf5.pc (hdf5.pc) in auto mode
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Processing triggers for libc-bin (2.33-7+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.38-4+rpi1 dpkg-dev_1.21.8+rpi1 g++-11_11.3.0-1+rpi1 gcc-11_11.3.0-1+rpi1 libc6-dev_2.33-7+rpi1 libstdc++-11-dev_11.3.0-1+rpi1 libstdc++6_12.1.0-2+rpi1 linux-libc-dev_5.18.2-1+rpi1
Package versions: adduser_3.121 apt_2.5.0 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6.1 binutils_2.38-4+rpi1 binutils-arm-linux-gnueabihf_2.38-4+rpi1 binutils-common_2.38-4+rpi1 bsdextrautils_2.38-4 bsdutils_1:2.38-4 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.3.0-1+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.8 debianutils_5.7-0.2 dh-autoreconf_20 dh-python_5.20220403 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.35-2 dpkg_1.21.8+rpi1 dpkg-dev_1.21.8+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:11.2.0-2+rpi1 g++-11_11.3.0-1+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.3.0-1+rpi1 gcc-11-base_11.3.0-1+rpi1 gcc-12-base_12.1.0-2+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-6 gettext-base_0.21-6 gnupg_2.2.35-2 gnupg-l10n_2.2.35-2 gnupg-utils_2.2.35-2 gpg_2.2.35-2 gpg-agent_2.2.35-2 gpg-wks-client_2.2.35-2 gpg-wks-server_2.2.35-2 gpgconf_2.2.35-2 gpgsm_2.2.35-2 gpgv_2.2.35-2 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hdf5-helpers_1.10.7+repack-4+rpi1+b1 hostname_3.23 init-system-helpers_1.63 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 krb5-locales_1.19.2-2 libacl1_2.3.1-1 libaec-dev_1.0.6-1 libaec0_1.0.6-1 libapt-pkg6.0_2.5.0 libarchive-zip-perl_1.68-1 libasan6_11.3.0-1+rpi1 libassuan0_2.5.5-3 libatomic1_12.1.0-2+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38-4+rpi1 libblkid1_2.38-4 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.33-7+rpi1 libc-dev-bin_2.33-7+rpi1 libc6_2.33-7+rpi1 libc6-dev_2.33-7+rpi1 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.1.0-2+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-4+rpi1 libctf0_2.38-4+rpi1 libcurl3-gnutls_7.83.1-2 libcurl4_7.83.1-2 libcurl4-gnutls-dev_7.83.1-2 libdb5.3_5.3.28+dfsg1-0.9 libdebconfclient0_0.263 libdebhelper-perl_13.8 libdeflate-dev_1.12-1 libdeflate0_1.12-1 libdpkg-perl_1.21.8+rpi1 libeigen3-dev_3.4.0-3 libelf1_0.187-1 libexpat1_2.4.8-1 libext2fs2_1.46.5-2 libfakeroot_1.29-1 libfast5-dev_0.6.5-7 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.3.0-1+rpi1 libgcc-s1_12.1.0-2+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran5_12.1.0-2+rpi1 libglib2.0-0_2.72.3-1 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.4-2 libgomp1_12.1.0-2+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.19.2-2+b7 libhdf5-103-1_1.10.7+repack-4+rpi1+b1 libhdf5-cpp-103-1_1.10.7+repack-4+rpi1+b1 libhdf5-dev_1.10.7+repack-4+rpi1+b1 libhdf5-fortran-102_1.10.7+repack-4+rpi1+b1 libhdf5-hl-100_1.10.7+repack-4+rpi1+b1 libhdf5-hl-cpp-100_1.10.7+repack-4+rpi1+b1 libhdf5-hl-fortran-100_1.10.7+repack-4+rpi1+b1 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2+b1 libhts3_1.13+ds-2+b1 libhtscodecs2_1.2.2-1 libicu71_71.1-3 libidn2-0_2.3.2-2 libisl23_0.24-2 libjpeg-dev_1:2.1.2-1 libjpeg62-turbo_1:2.1.2-1 libjpeg62-turbo-dev_1:2.1.2-1 libk5crypto3_1.19.2-2+b7 libkeyutils1_1.6.1-3+rpi1 libkrb5-3_1.19.2-2+b7 libkrb5support0_1.19.2-2+b7 libksba8_1.6.0-2 libldap-2.5-0_2.5.12+dfsg-2 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2.1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libminimap2-dev_2.24+dfsg-2 libmount1_2.38-4 libmpc3_1.2.1-2 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.3+20220423-2 libnettle8_3.7.3-1 libnghttp2-14_1.47.0-1+b1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.4.0-13 libpam-modules-bin_1.4.0-13 libpam-runtime_1.4.0-13 libpam0g_1.4.0-13 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-4 libpipeline1_1.5.6-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.10.4-1+b1 libpython3.10-minimal_3.10.5-1+b1 libpython3.10-stdlib_3.10.5-1+b1 libreadline8_8.1.2-1.2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-6+b1 libsasl2-modules-db_2.1.28+dfsg-6+b1 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsigsegv2_2.14-1 libslow5-0_0.5.1+dfsg-2 libslow5-dev_0.5.1+dfsg-2 libsmartcols1_2.38-4 libsqlite3-0_3.38.5-1 libss2_1.46.5-2 libssh2-1_1.10.0-3+b1 libssl-dev_3.0.4-2 libssl1.1_1.1.1o-1 libssl3_3.0.4-2 libstdc++-11-dev_11.3.0-1+rpi1 libstdc++6_12.1.0-2+rpi1 libstreamvbyte-dev_0.4.1-4 libstreamvbyte0_0.4.1-4 libsub-override-perl_0.09-3 libsystemd0_250.4-1+rpi1 libsz2_1.0.6-1 libtasn1-6_4.18.0-4 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-4 libubsan1_12.1.0-2+rpi1 libuchardet0_0.0.7-1 libudev1_250.4-1+rpi1 libunistring2_1.0-1 libuuid1_2.38-4 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.18.2-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.2+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3.1 media-types_8.0.0 mount_2.38-4 nano_6.3-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-4 perl-base_5.34.0-4 perl-modules-5.34_5.34.0-4 pinentry-curses_1.2.0-1 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 python3_3.10.4-1+b1 python3-distutils_3.9.12-1 python3-lib2to3_3.9.12-1 python3-minimal_3.10.4-1+b1 python3.10_3.10.5-1+b1 python3.10-minimal_3.10.5-1+b1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-nanopolish-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.03-1 tar_1.34+dfsg-1 tzdata_2022a-1 util-linux_2.38-4 util-linux-extra_2.38-4 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4+b2 zlib1g-dev_1:1.2.11.dfsg-4+b2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.IlkkXTyk/trustedkeys.kbx': General error
gpgv: Signature made Sat Jul 9 18:18:20 2022 UTC
gpgv: using RSA key 3E99A526F5DCC0CBBF1CEEA600BAE74B343369F1
gpgv: issuer "nilesh@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./nanopolish_0.14.0-1.dsc
dpkg-source: info: extracting nanopolish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking nanopolish_0.14.0.orig.tar.gz
dpkg-source: info: unpacking nanopolish_0.14.0-1.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
dpkg-source: info: applying link_ext_slow5lib.patch
Check disk 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=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-78679256-3881-46b8-99af-072096909e77
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package nanopolish
dpkg-buildpackage: info: source version 0.14.0-1
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/basemods/nanopolish_basemods.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_detect_polyi.o src/nanopolish_fast5_check.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
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f ./.depend
g++ -g -O2 -ffile-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./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./src/basemods -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/basemods/nanopolish_basemods.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_detect_polyi.cpp src/nanopolish_fast5_check.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/main/nanopolish.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/main/nanopolish.cpp
g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/alignment/nanopolish_alignment_db.cpp
g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/alignment/nanopolish_anchor.cpp
g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/alignment/nanopolish_eventalign.cpp
g++ -o src/basemods/nanopolish_basemods.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/basemods/nanopolish_basemods.cpp
g++ -o src/common/fs_support.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/fs_support.cpp
g++ -o src/common/logsum.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/logsum.cpp
g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/nanopolish_alphabet.cpp
g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/nanopolish_bam_processor.cpp
g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/nanopolish_bam_utils.cpp
g++ -o src/common/nanopolish_common.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/nanopolish_common.cpp
g++ -o src/common/nanopolish_iupac.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/nanopolish_iupac.cpp
g++ -o src/common/nanopolish_klcs.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/nanopolish_klcs.cpp
g++ -o src/common/nanopolish_variant.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/common/nanopolish_variant.cpp
g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/hmm/nanopolish_duration_model.cpp
g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/hmm/nanopolish_profile_hmm.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r7.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:210:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
210 | 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_r9.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp
g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/hmm/nanopolish_transition_parameters.cpp
g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/io/nanopolish_fast5_io.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:162:28: warning: narrowing conversion of 'nsample' from 'hsize_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing]
162 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
| ^~~~~~~
src/io/nanopolish_fast5_io.cpp:162:40: warning: narrowing conversion of 'nsample' from 'hsize_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing]
162 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
| ^~~~~~~
g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/io/nanopolish_fast5_loader.cpp
g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/io/nanopolish_fast5_processor.cpp
g++ -o src/nanopolish_call_methylation.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_call_methylation.cpp
src/io/nanopolish_fast5_loader.cpp: In static member function 'static Fast5Data Fast5Loader::load_read(slow5_file_t*, const string&)':
src/io/nanopolish_fast5_loader.cpp:94:34: warning: narrowing conversion of 'rec->slow5_rec::len_raw_signal' from 'uint64_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing]
94 | data.rt = (raw_table) { rec->len_raw_signal, 0, rec->len_raw_signal, rawptr };
| ~~~~~^~~~~~~~~~~~~~
src/io/nanopolish_fast5_loader.cpp:94:58: warning: narrowing conversion of 'rec->slow5_rec::len_raw_signal' from 'uint64_t' {aka 'long long unsigned int'} to 'size_t' {aka 'unsigned int'} [-Wnarrowing]
94 | data.rt = (raw_table) { rec->len_raw_signal, 0, rec->len_raw_signal, rawptr };
| ~~~~~^~~~~~~~~~~~~~
g++ -o src/nanopolish_call_variants.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_call_variants.cpp
g++ -o src/nanopolish_detect_polyi.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_detect_polyi.cpp
g++ -o src/nanopolish_fast5_check.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_fast5_check.cpp
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
src/nanopolish_detect_polyi.cpp: In function 'void dpi_estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)':
src/nanopolish_detect_polyi.cpp:1040:39: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long long int' [-Wformat=]
1040 | fprintf(out_fp, "%s\t%s\t%d\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n",
| ~^
| |
| int
| %lld
1041 | read_name.c_str(), ref_name.c_str(), record->core.pos);
| ~~~~~~~~~~~~~~~~
| |
| long long int
src/nanopolish_detect_polyi.cpp:1105:35: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long long int' [-Wformat=]
1105 | fprintf(out_fp, "%s\t%s\t%d\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\t%s\n",
| ~^
| |
| int
| %lld
1106 | read_name.c_str(), ref_name.c_str(), record->core.pos,
| ~~~~~~~~~~~~~~~~
| |
| long long int
g++ -o src/nanopolish_haplotype.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_haplotype.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 'unsigned int' [-Wformat=]
172 | fprintf(stderr, "[haplotype-debug] ctg: %s, position: %lu\n", m_ref_name.c_str(), m_ref_position);
| ~~^ ~~~~~~~~~~~~~~
| | |
| long unsigned int unsigned int
| %u
g++ -o src/nanopolish_index.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_index.cpp
g++ -o src/nanopolish_methyltrain.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_methyltrain.cpp
g++ -o src/nanopolish_phase_reads.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_phase_reads.cpp
g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_polya_estimator.cpp
src/nanopolish_index.cpp: In function 'int index_main(int, char**)':
src/nanopolish_index.cpp:386:72: warning: format '%ld' expects argument of type 'long int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
386 | fprintf(stderr,"fast5 files could not be located for %ld reads\n",num_reads-num_with_path);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long int size_t {aka unsigned int}
| %d
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:765:39: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long long int' [-Wformat=]
765 | fprintf(out_fp, "%s\t%s\t%d\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n",
| ~^
| |
| int
| %lld
766 | read_name.c_str(), ref_name.c_str(), record->core.pos);
| ~~~~~~~~~~~~~~~~
| |
| long long int
src/nanopolish_polya_estimator.cpp:823:35: warning: format '%d' expects argument of type 'int', but argument 5 has type 'long long int' [-Wformat=]
823 | fprintf(out_fp, "%s\t%s\t%d\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\n",
| ~^
| |
| int
| %lld
824 | read_name.c_str(), ref_name.c_str(), record->core.pos,
| ~~~~~~~~~~~~~~~~
| |
| long long int
g++ -o src/nanopolish_raw_loader.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_raw_loader.cpp
g++ -o src/nanopolish_read_db.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_read_db.cpp
g++ -o src/nanopolish_scorereads.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_scorereads.cpp
g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_squiggle_read.cpp
g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp
g++ -o src/nanopolish_variant_db.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_variant_db.cpp
g++ -o src/nanopolish_vcf2fasta.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/nanopolish_vcf2fasta.cpp
g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/pore_model/nanopolish_model_names.cpp
g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/pore_model/nanopolish_pore_model_set.cpp
g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/pore_model/nanopolish_poremodel.cpp
g++ -o src/training_core.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/training_core.cpp
cc -o src/thirdparty/fet.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/thirdparty/fet.c
cc -o src/thirdparty/scrappie/event_detection.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/thirdparty/scrappie/event_detection.c
cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/thirdparty/scrappie/scrappie_common.c
cc -o src/thirdparty/stdaln.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/thirdparty/stdaln.c
g++ -o nanopolish -g -O2 -ffile-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./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./src/basemods -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.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_detect_polyi.o src/nanopolish_fast5_check.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 -lslow5 -lstreamvbyte -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
/usr/bin/make nanopolish_test
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -o src/test/nanopolish_test.o -c -g -O2 -ffile-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./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./src/basemods -fPIC src/test/nanopolish_test.cpp
g++ -o nanopolish_test -g -O2 -ffile-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./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./src/basemods -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/basemods/nanopolish_basemods.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_detect_polyi.o src/nanopolish_fast5_check.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 -lslow5 -lstreamvbyte -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "Since we need the executable created inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck."
Since we need the executable created inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck.
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_auto_install --destdir=debian/nanopolish/ -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/lib/nanopolish/nanopolish_test contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
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: package could avoid a useless dependency if debian/nanopolish/usr/lib/nanopolish/nanopolish_test debian/nanopolish/usr/bin/nanopolish were not linked against libstreamvbyte.so.0 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'nanopolish-dbgsym' in '../nanopolish-dbgsym_0.14.0-1_armhf.deb'.
dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-1_armhf.deb'.
dpkg-genbuildinfo --build=any -O../nanopolish_0.14.0-1_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../nanopolish_0.14.0-1_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 2022-07-17T05:52:15Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
nanopolish_0.14.0-1_armhf.changes:
----------------------------------
Format: 1.8
Date: Sat, 09 Jul 2022 23:37:52 +0530
Source: nanopolish
Binary: nanopolish nanopolish-dbgsym
Architecture: armhf
Version: 0.14.0-1
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Nilesh Patra <nilesh@debian.org>
Description:
nanopolish - consensus caller for nanopore sequencing data
Changes:
nanopolish (0.14.0-1) unstable; urgency=medium
.
* Team Upload.
.
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
.
[ Nilesh Patra ]
* Add opt to link against external slow5lib
* B-D on libslow5lib
* d/rules: export SLOW5LIB=external
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be3da38d9ee2ab76f03b2a8a7cf748eeef21f367 7108 nanopolish_0.14.0-1_armhf.buildinfo
333eb3e6538c31ef424ffac6cceba8bade361bf5 2127664 nanopolish_0.14.0-1_armhf.deb
Checksums-Sha256:
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aee912d9740d3cf000d966476cb0989ac0fb1529c96b5fc38d05dcffc3534643 7108 nanopolish_0.14.0-1_armhf.buildinfo
b8531a0fcfe8d8b05a592d2d4c8c8a3c4c57acb1f78603be2b86a19edb93cfc3 2127664 nanopolish_0.14.0-1_armhf.deb
Files:
86bba5533620398e2a5ab280516d3296 6113568 debug optional nanopolish-dbgsym_0.14.0-1_armhf.deb
2f67e24b70b9c9817b2efaecc8ef0b98 7108 science optional nanopolish_0.14.0-1_armhf.buildinfo
e8ce78305940db4659cdeea714242f6d 2127664 science optional nanopolish_0.14.0-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
nanopolish-dbgsym_0.14.0-1_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 6113568 bytes: control archive=648 bytes.
426 bytes, 12 lines control
302 bytes, 3 lines md5sums
Package: nanopolish-dbgsym
Source: nanopolish
Version: 0.14.0-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6364
Depends: nanopolish (= 0.14.0-1)
Section: debug
Priority: optional
Description: debug symbols for nanopolish
Build-Ids: 3d09cd222d7bcb28171d107677bf7bbebe9daac8 a73df479feae9604d294396ddf1fea4b89e4961a
drwxr-xr-x root/root 0 2022-07-09 18:07 ./
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.build-id/3d/
-rw-r--r-- root/root 2008916 2022-07-09 18:07 ./usr/lib/debug/.build-id/3d/09cd222d7bcb28171d107677bf7bbebe9daac8.debug
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.build-id/a7/
-rw-r--r-- root/root 2272388 2022-07-09 18:07 ./usr/lib/debug/.build-id/a7/3df479feae9604d294396ddf1fea4b89e4961a.debug
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 2220284 2022-07-09 18:07 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/nanopolish.debug
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/
drwxr-xr-x root/root 0 2022-07-09 18:07 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-07-09 18:07 ./usr/share/doc/nanopolish-dbgsym -> nanopolish
nanopolish_0.14.0-1_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 2127664 bytes: control archive=2156 bytes.
951 bytes, 18 lines control
2320 bytes, 30 lines md5sums
305 bytes, 12 lines * postinst #!/bin/sh
411 bytes, 12 lines * prerm #!/bin/sh
Package: nanopolish
Version: 0.14.0-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9213
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libhdf5-103-1, libhts3 (>= 1.10), libslow5-0 (>= 0.5.1+dfsg), libstdc++6 (>= 11), libstreamvbyte0 (>= 0.4.1), 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.
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-rw-r--r-- root/root 2592 2022-07-09 18:07 ./usr/lib/nanopolish/import_ont_model.py
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-rw-r--r-- root/root 4915 2022-07-09 18:07 ./usr/lib/nanopolish/polya_training/dump_signal.py
-rw-r--r-- root/root 2248 2022-04-19 15:17 ./usr/lib/nanopolish/polya_training/environment.yml
-rw-r--r-- root/root 4739 2022-07-09 18:07 ./usr/lib/nanopolish/polya_training/hmmplot.py
-rw-r--r-- root/root 4071 2022-07-09 18:07 ./usr/lib/nanopolish/polya_training/retrain_emission.py
-rw-r--r-- root/root 4029 2022-07-09 18:07 ./usr/lib/nanopolish/polya_training/workflow.md
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-rw-r--r-- root/root 4071 2022-07-02 09:08 ./usr/share/doc/nanopolish/copyright
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Build Architecture: armhf
Build-Space: 116304
Build-Time: 349
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 250
Job: nanopolish_0.14.0-1
Machine Architecture: armhf
Package: nanopolish
Package-Time: 621
Source-Version: 0.14.0-1
Space: 116304
Status: successful
Version: 0.14.0-1
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Finished at 2022-07-17T05:52:15Z
Build needed 00:10:21, 116304k disk space