nanopolish →
0.14.0-1+b2 →
armhf → 2024-01-19 17:11:59
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| nanopolish 0.14.0-1+b2 (armhf) Fri, 19 Jan 2024 17:08:38 +0000 |
+==============================================================================+
Package: nanopolish
Version: 0.14.0-1+b2
Source Version: 0.14.0-1
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-77c2dacc-6845-4de9-bd0b-4d7a92ee531e' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/nanopolish-flmwq2/resolver-Hod73l' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.4 MB in 5s (5558 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-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 trixie-staging/main nanopolish 0.14.0-1 (dsc) [2114 B]
Get:2 http://172.17.4.1/private trixie-staging/main nanopolish 0.14.0-1 (tar) [4074 kB]
Get:3 http://172.17.4.1/private trixie-staging/main nanopolish 0.14.0-1 (diff) [8976 B]
Fetched 4085 kB in 1s (7682 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/nanopolish-flmwq2/nanopolish-0.14.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/nanopolish-flmwq2' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| 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, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [741 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [773 B]
Fetched 2123 B in 0s (0 B/s)
Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils cpp-13
debhelper dh-autoreconf dh-python dh-strip-nondeterminism dwz file g++-13
gcc-13 gcc-13-base gettext gettext-base groff-base hdf5-helpers
intltool-debian libaec-dev libaec0 libarchive-zip-perl libasan8 libatomic1
libblkid1 libbrotli1 libcc1-0 libcurl3-gnutls libcurl4 libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfast5-dev libfile-stripnondeterminism-perl libgcc-13-dev libgcc-s1
libgfortran5 libgomp1 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 libicu72 libjpeg-dev libjpeg62-turbo
libjpeg62-turbo-dev liblzma-dev liblzma5 libmagic-mgc libmagic1
libminimap2-dev libmount1 libnghttp2-14 libpipeline1 libpkgconf3 libpsl5
libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1
libslow5-0 libslow5-dev libsmartcols1 libssh2-1 libssl-dev libstdc++-13-dev
libstdc++6 libstreamvbyte-dev libstreamvbyte0 libsub-override-perl libsz2
libtool libubsan1 libuchardet0 libuuid1 libxml2 m4 man-db media-types mount
netbase pkg-config pkgconf pkgconf-bin po-debconf python3 python3-distutils
python3-lib2to3 python3-minimal python3-pkg-resources python3-setuptools
python3.11 python3.11-minimal sensible-utils util-linux xz-utils zlib1g
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-13-locales cpp-13-doc
dh-make flit python3-build python3-installer python3-wheel gcc-13-doc
gettext-doc libasprintf-dev libgettextpo-dev groff libcurl4-doc
libgnutls28-dev libidn-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev libeigen3-doc libmpfrc++-dev libhdf5-doc liblzma-doc
cryptsetup-bin libssl-doc libstdc++-13-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser nfs-common
libmail-box-perl python3-doc python3-tk python3-venv python-setuptools-doc
python3.11-venv python3.11-doc binfmt-support dosfstools kbd
util-linux-extra util-linux-locales
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl publicsuffix
libltdl-dev uuid-runtime 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 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
libicu72 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblzma-dev
libmagic-mgc libmagic1 libminimap2-dev libnghttp2-14 libpipeline1
libpkgconf3 libpsl5 libpython3-stdlib libpython3.11-minimal
libpython3.11-stdlib librtmp1 libslow5-0 libslow5-dev libssh2-1 libssl-dev
libstreamvbyte-dev libstreamvbyte0 libsub-override-perl libsz2 libtool
libuchardet0 libxml2 m4 man-db media-types netbase pkg-config pkgconf
pkgconf-bin po-debconf python3 python3-distutils python3-lib2to3
python3-minimal python3-pkg-resources python3-setuptools python3.11
python3.11-minimal sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
The following packages will be upgraded:
bsdutils cpp-13 g++-13 gcc-13 gcc-13-base libasan8 libatomic1 libblkid1
libcc1-0 libgcc-13-dev libgcc-s1 libgomp1 liblzma5 libmount1 libsmartcols1
libstdc++-13-dev libstdc++6 libubsan1 libuuid1 mount util-linux xz-utils
zlib1g
23 upgraded, 88 newly installed, 0 to remove and 24 not upgraded.
Need to get 77.3 MB of archives.
After this operation, 146 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [928 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.3-6 [87.1 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.3-6 [1113 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.3-6 [134 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.7-2 [801 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf libcc1-0 armhf 13.2.0-9+rpi1 [35.4 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf gcc-13-base armhf 13.2.0-9+rpi1 [41.7 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libgcc-s1 armhf 13.2.0-9+rpi1 [36.2 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libgomp1 armhf 13.2.0-9+rpi1 [104 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libatomic1 armhf 13.2.0-9+rpi1 [8448 B]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libasan8 armhf 13.2.0-9+rpi1 [2391 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf libubsan1 armhf 13.2.0-9+rpi1 [964 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf g++-13 armhf 13.2.0-9+rpi1 [8138 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libstdc++-13-dev armhf 13.2.0-9+rpi1 [2209 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf libgcc-13-dev armhf 13.2.0-9+rpi1 [763 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf gcc-13 armhf 13.2.0-9+rpi1 [14.7 MB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf cpp-13 armhf 13.2.0-9+rpi1 [7372 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libstdc++6 armhf 13.2.0-9+rpi1 [578 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf zlib1g armhf 1:1.3.dfsg-3 [74.3 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.7-2 [1677 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf netbase all 6.4 [12.8 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf liblzma5 armhf 5.4.5-0.3 [227 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.3-6 [28.3 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.7-2 [1694 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.7-2 [590 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
Get:30 http://172.17.4.1/private trixie-staging/main armhf python3 armhf 3.11.4-5 [26.2 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.3-6 [145 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.3-6 [168 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.3-6 [102 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.20 [19.3 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf xz-utils armhf 5.4.5-0.3 [499 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.9 [82.3 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:57 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.9 [956 kB]
Get:65 http://172.17.4.1/private trixie-staging/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB]
Get:66 http://172.17.4.1/private trixie-staging/main armhf python3-distutils all 3.11.5-1 [131 kB]
Get:67 http://172.17.4.1/private trixie-staging/main armhf python3-pkg-resources all 68.1.2-2 [241 kB]
Get:68 http://172.17.4.1/private trixie-staging/main armhf python3-setuptools all 68.1.2-2 [468 kB]
Get:69 http://172.17.4.1/private trixie-staging/main armhf dh-python all 6.20231223 [108 kB]
Get:70 http://172.17.4.1/private trixie-staging/main armhf hdf5-helpers armhf 1.10.10+repack-3 [23.2 kB]
Get:71 http://172.17.4.1/private trixie-staging/main armhf libaec0 armhf 1.1.2-1 [21.3 kB]
Get:72 http://172.17.4.1/private trixie-staging/main armhf libsz2 armhf 1.1.2-1 [7700 B]
Get:73 http://172.17.4.1/private trixie-staging/main armhf libaec-dev armhf 1.1.2-1 [18.4 kB]
Get:74 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:75 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:76 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:77 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:78 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-4 [195 kB]
Get:79 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.5.0-2+rpi1 [372 kB]
Get:80 http://172.17.4.1/private trixie-staging/main armhf libcurl4 armhf 8.5.0-2+rpi1 [377 kB]
Get:81 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 8.5.0-2+rpi1 [456 kB]
Get:82 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:83 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.18-1 [45.8 kB]
Get:84 http://172.17.4.1/private trixie-staging/main armhf libpkgconf3 armhf 1.8.1-1 [31.3 kB]
Get:85 http://172.17.4.1/private trixie-staging/main armhf pkgconf-bin armhf 1.8.1-1 [27.8 kB]
Get:86 http://172.17.4.1/private trixie-staging/main armhf pkgconf armhf 1.8.1-1 [25.9 kB]
Get:87 http://172.17.4.1/private trixie-staging/main armhf pkg-config armhf 1.8.1-1 [13.7 kB]
Get:88 http://172.17.4.1/private trixie-staging/main armhf libeigen3-dev all 3.4.0-4 [1041 kB]
Get:89 http://172.17.4.1/private trixie-staging/main armhf libhdf5-103-1 armhf 1.10.10+repack-3 [1215 kB]
Get:90 http://172.17.4.1/private trixie-staging/main armhf libgfortran5 armhf 13.2.0-9+rpi1 [247 kB]
Get:91 http://172.17.4.1/private trixie-staging/main armhf libhdf5-fortran-102 armhf 1.10.10+repack-3 [77.3 kB]
Get:92 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-100 armhf 1.10.10+repack-3 [59.9 kB]
Get:93 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.10+repack-3 [34.1 kB]
Get:94 http://172.17.4.1/private trixie-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.10+repack-3 [112 kB]
Get:95 http://172.17.4.1/private trixie-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.10+repack-3 [20.5 kB]
Get:96 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
Get:97 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo armhf 1:2.1.5-2 [143 kB]
Get:98 http://172.17.4.1/private trixie-staging/main armhf libjpeg62-turbo-dev armhf 1:2.1.5-2 [258 kB]
Get:99 http://172.17.4.1/private trixie-staging/main armhf libjpeg-dev armhf 1:2.1.5-2 [71.8 kB]
Get:100 http://172.17.4.1/private trixie-staging/main armhf libssl-dev armhf 3.1.4-2 [2115 kB]
Get:101 http://172.17.4.1/private trixie-staging/main armhf libhdf5-dev armhf 1.10.10+repack-3 [2314 kB]
Get:102 http://172.17.4.1/private trixie-staging/main armhf libfast5-dev all 0.6.5-7 [50.2 kB]
Get:103 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.6.0-1 [60.3 kB]
Get:104 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.18+ds-1 [380 kB]
Get:105 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.5-0.3 [278 kB]
Get:106 http://172.17.4.1/private trixie-staging/main armhf libhts-dev armhf 1.18+ds-1 [1539 kB]
Get:107 http://172.17.4.1/private trixie-staging/main armhf libminimap2-dev armhf 2.24+dfsg-3+b1 [123 kB]
Get:108 http://172.17.4.1/private trixie-staging/main armhf libslow5-0 armhf 0.7.0+dfsg-2 [57.2 kB]
Get:109 http://172.17.4.1/private trixie-staging/main armhf libslow5-dev armhf 0.7.0+dfsg-2 [67.3 kB]
Get:110 http://172.17.4.1/private trixie-staging/main armhf libstreamvbyte0 armhf 0.4.1-4 [5120 B]
Get:111 http://172.17.4.1/private trixie-staging/main armhf libstreamvbyte-dev armhf 0.4.1-4 [6032 B]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 12735 files and directories currently installed.)
Preparing to unpack .../bsdutils_1%3a2.39.3-6_armhf.deb ...
Unpacking bsdutils (1:2.39.3-6) over (1:2.39.3-2) ...
Setting up bsdutils (1:2.39.3-6) ...
(Reading database ... 12735 files and directories currently installed.)
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Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-14) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-2) ...
Setting up libgomp1:armhf (13.2.0-9+rpi1) ...
Setting up libaec0:armhf (1.1.2-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libpkgconf3:armhf (1.8.1-1) ...
Setting up libjpeg62-turbo:armhf (1:2.1.5-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.1.5-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up xz-utils (5.4.5-0.3) ...
Setting up libstreamvbyte-dev:armhf (0.4.1-4) ...
Setting up libssl-dev:armhf (3.1.4-2) ...
Setting up autopoint (0.21-14) ...
Setting up libslow5-0:armhf (0.7.0+dfsg-2) ...
Setting up pkgconf-bin (1.8.1-1) ...
Setting up libgfortran5:armhf (13.2.0-9+rpi1) ...
Setting up autoconf (2.71-3) ...
Setting up liblzma-dev:armhf (5.4.5-0.3) ...
Setting up libubsan1:armhf (13.2.0-9+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.3.dfsg-3) ...
Setting up mount (2.39.3-6) ...
Setting up sensible-utils (0.0.20) ...
Setting up libasan8:armhf (13.2.0-9+rpi1) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libssh2-1:armhf (1.11.0-4) ...
Setting up netbase (6.4) ...
Setting up libdeflate-dev:armhf (1.18-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up libcc1-0:armhf (13.2.0-9+rpi1) ...
Setting up libsz2:armhf (1.1.2-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-14) ...
Setting up libtool (2.4.7-7) ...
Setting up libpython3.11-stdlib:armhf (3.11.7-2) ...
Setting up libaec-dev:armhf (1.1.2-1) ...
Setting up libjpeg-dev:armhf (1:2.1.5-2) ...
Setting up libcurl3-gnutls:armhf (8.5.0-2+rpi1) ...
Setting up libslow5-dev:armhf (0.7.0+dfsg-2) ...
Setting up libcurl4-gnutls-dev:armhf (8.5.0-2+rpi1) ...
Setting up pkgconf:armhf (1.8.1-1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up libminimap2-dev (2.24+dfsg-3+b1) ...
Setting up libeigen3-dev (3.4.0-4) ...
Setting up pkg-config:armhf (1.8.1-1) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up libgcc-13-dev:armhf (13.2.0-9+rpi1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libcurl4:armhf (8.5.0-2+rpi1) ...
Setting up libstdc++-13-dev:armhf (13.2.0-9+rpi1) ...
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up python3.11 (3.11.7-2) ...
Setting up libhts3:armhf (1.18+ds-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.18+ds-1) ...
Setting up python3 (3.11.4-5) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gcc-13 (13.2.0-9+rpi1) ...
Setting up libhdf5-103-1:armhf (1.10.10+repack-3) ...
Setting up libhdf5-cpp-103-1:armhf (1.10.10+repack-3) ...
Setting up python3-lib2to3 (3.11.5-1) ...
Setting up libhdf5-hl-100:armhf (1.10.10+repack-3) ...
Setting up python3-pkg-resources (68.1.2-2) ...
Setting up python3-distutils (3.11.5-1) ...
Setting up g++-13 (13.2.0-9+rpi1) ...
Setting up python3-setuptools (68.1.2-2) ...
Setting up debhelper (13.11.9) ...
Setting up libhdf5-hl-cpp-100:armhf (1.10.10+repack-3) ...
Setting up libhdf5-fortran-102:armhf (1.10.10+repack-3) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.10+repack-3) ...
Setting up dh-python (6.20231223) ...
Setting up libhdf5-dev (1.10.10+repack-3) ...
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
Setting up libfast5-dev (0.6.5-7) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.9 debianutils_5.14 dh-autoreconf_20 dh-python_6.20231223 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-9+rpi1 gcc-13-base_13.2.0-9+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_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hdf5-helpers_1.10.10+repack-3 hostname_3.23+nmu1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libaec-dev_1.1.2-1 libaec0_1.1.2-1 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-9+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-9+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-6 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-3 libcap2_1:2.66-4 libcc1-0_13.2.0-9+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.5.0-2+rpi1 libcurl4_8.5.0-2+rpi1 libcurl4-gnutls-dev_8.5.0-2+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.9 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libeigen3-dev_3.4.0-4 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.2-1 libfast5-dev_0.6.5-7 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-9+rpi1 libgcc-s1_13.2.0-9+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgfortran5_13.2.0-9+rpi1 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-9+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhdf5-103-1_1.10.10+repack-3 libhdf5-cpp-103-1_1.10.10+repack-3 libhdf5-dev_1.10.10+repack-3 libhdf5-fortran-102_1.10.10+repack-3 libhdf5-hl-100_1.10.10+repack-3 libhdf5-hl-cpp-100_1.10.10+repack-3 libhdf5-hl-fortran-100_1.10.10+repack-3 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1 libhts3_1.18+ds-1 libhtscodecs2_1.6.0-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjpeg-dev_1:2.1.5-2 libjpeg62-turbo_1:2.1.5-2 libjpeg62-turbo-dev_1:2.1.5-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblocale-gettext-perl_1.07-6 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.5-0.3 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libminimap2-dev_2.24+dfsg-3+b1 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-2 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libperl5.36_5.36.0-10 libpipeline1_1.5.7-1 libpkgconf3_1.8.1-1 libpsl5_0.21.2-1+b1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.7-2 libpython3.11-stdlib_3.11.7-2 libreadline8_8.2-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libslow5-0_0.7.0+dfsg-2 libslow5-dev_0.7.0+dfsg-2 libsmartcols1_2.39.3-6 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-4 libssl-dev_3.1.4-2 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 libstreamvbyte-dev_0.4.1-4 libstreamvbyte0_0.4.1-4 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libsz2_1.1.2-1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11 libtext-glob-perl_0.11-3 libtext-iconv-perl_1.7-8 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-9+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.3-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 media-types_10.1.0 mount_2.39.3-6 nano_7.2-1 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 netbase_6.4 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-10 perl-base_5.36.0-10 perl-modules-5.36_5.36.0-10 pinentry-curses_1.2.1-3 pkg-config_1.8.1-1 pkgconf_1.8.1-1 pkgconf-bin_1.8.1-1 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-distutils_3.11.5-1 python3-lib2to3_3.11.5-1 python3-minimal_3.11.4-5 python3-pkg-resources_68.1.2-2 python3-setuptools_68.1.2-2 python3.11_3.11.7-2 python3.11-minimal_3.11.7-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-5 tar_1.34+dfsg-1.3 tzdata_2023c-11 usr-is-merged_38 usrmerge_38 util-linux_2.39.3-6 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: nanopolish
Binary: nanopolish
Architecture: any
Version: 0.14.0-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/jts/nanopolish
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/nanopolish
Vcs-Git: https://salsa.debian.org/med-team/nanopolish.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), dh-python, python3, zlib1g-dev, libfast5-dev, libhts-dev, libeigen3-dev, libminimap2-dev, libstreamvbyte-dev, libslow5-dev
Package-List:
nanopolish deb science optional arch=any
Checksums-Sha1:
a26c2a1a0f41a0e3fef52dee3d6ef1aea11e0266 4073583 nanopolish_0.14.0.orig.tar.gz
70b1db592822052179b1c679ea8999f0af4c5e94 8976 nanopolish_0.14.0-1.debian.tar.xz
Checksums-Sha256:
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6c5a39be2682ee430fcc2daf99c7574adf9f0110d4caa13f29af767a995d5bfe 8976 nanopolish_0.14.0-1.debian.tar.xz
Files:
90b445d40348427fd009bea3e04f0249 4073583 nanopolish_0.14.0.orig.tar.gz
f33e6f1fb88a7cbe9d018781b5d2758c 8976 nanopolish_0.14.0-1.debian.tar.xz
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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 inline signature for ./nanopolish_0.14.0-1.dsc: no acceptable signature found
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
Hack binNMU version
-------------------
Created changelog entry for binNMU version 0.14.0-1+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-77c2dacc-6845-4de9-bd0b-4d7a92ee531e
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package nanopolish
dpkg-buildpackage: info: source version 0.14.0-1+b2
dpkg-buildpackage: info: source distribution trixie-staging
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++ -o src/main/nanopolish.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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/alignment/nanopolish_anchor.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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
g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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
src/io/nanopolish_fast5_io.cpp: In function ‘raw_table fast5_get_raw_samples(fast5_file&, const std::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/nanopolish_call_methylation.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
g++ -o src/nanopolish_call_variants.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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
src/io/nanopolish_fast5_loader.cpp: In static member function ‘static Fast5Data Fast5Loader::load_read(slow5_file_t*, const std::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_detect_polyi.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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 -fstack-clash-protection -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
lto-wrapper: warning: using serial compilation of 11 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
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 -fstack-clash-protection -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 -fstack-clash-protection -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
lto-wrapper: warning: using serial compilation of 8 LTRANS jobs
lto-wrapper: note: see the ‘-flto’ option documentation for more information
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/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
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/nanopolish/usr/bin/nanopolish debian/nanopolish/usr/lib/nanopolish/nanopolish_test were not linked against libstreamvbyte.so.0 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/nanopolish/usr/bin/nanopolish debian/nanopolish/usr/lib/nanopolish/nanopolish_test were not linked against ld-linux-armhf.so.3 (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+b2_armhf.deb'.
dpkg-deb: building package 'nanopolish' in '../nanopolish_0.14.0-1+b2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../nanopolish_0.14.0-1+b2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi5 test autobuilder <root@raspbian.org> -O../nanopolish_0.14.0-1+b2_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 2024-01-19T17:11:54Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
nanopolish_0.14.0-1+b2_armhf.changes:
-------------------------------------
Format: 1.8
Date: Fri, 19 Jan 2024 17:10:10 +0000
Source: nanopolish (0.14.0-1)
Binary: nanopolish nanopolish-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 0.14.0-1+b2
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian pi5 test autobuilder <root@raspbian.org>
Changed-By: Raspbian pi5 test autobuilder <root@raspbian.org>
Description:
nanopolish - consensus caller for nanopore sequencing data
Changes:
nanopolish (0.14.0-1+b2) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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cb35b5d4e31b37fb52ca4565e87fbd9cc27e05d7 7758 nanopolish_0.14.0-1+b2_armhf.buildinfo
54607d243592a36d77ff420238390161d1b03180 2119084 nanopolish_0.14.0-1+b2_armhf.deb
Checksums-Sha256:
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4d2f4e54ffdd5b0c32269d3b975c3a36076d50ecb79ab5cd638152d990749a1f 7758 nanopolish_0.14.0-1+b2_armhf.buildinfo
f58cd5181c1200560f496e325179dee56bce5cecd640ed4f738184bea1b46952 2119084 nanopolish_0.14.0-1+b2_armhf.deb
Files:
bf6a07738c81535f088578678c2d6c71 5460328 debug optional nanopolish-dbgsym_0.14.0-1+b2_armhf.deb
c063d017905dea0c876276bd31ab433b 7758 science optional nanopolish_0.14.0-1+b2_armhf.buildinfo
9986e21c29758893f63c304a0cca7b7c 2119084 science optional nanopolish_0.14.0-1+b2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: nanopolish (0.14.0-1)
Binary: nanopolish nanopolish-dbgsym
Architecture: armhf
Version: 0.14.0-1+b2
Binary-Only-Changes:
nanopolish (0.14.0-1+b2) trixie-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
.
-- Raspbian pi5 test autobuilder <root@raspbian.org> Fri, 19 Jan 2024 17:10:10 +0000
Checksums-Md5:
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9986e21c29758893f63c304a0cca7b7c 2119084 nanopolish_0.14.0-1+b2_armhf.deb
Checksums-Sha1:
50194701903e2bc14323da418559f2216924b769 5460328 nanopolish-dbgsym_0.14.0-1+b2_armhf.deb
54607d243592a36d77ff420238390161d1b03180 2119084 nanopolish_0.14.0-1+b2_armhf.deb
Checksums-Sha256:
d149f7871da2f8b62aa83ab9815d67a3956c05e5b50e1d2181d37c38c972ab52 5460328 nanopolish-dbgsym_0.14.0-1+b2_armhf.deb
f58cd5181c1200560f496e325179dee56bce5cecd640ed4f738184bea1b46952 2119084 nanopolish_0.14.0-1+b2_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Fri, 19 Jan 2024 17:11:53 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
merged-usr-via-aliased-dirs
Installed-Build-Depends:
autoconf (= 2.71-3),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-14),
autotools-dev (= 20220109.1),
base-files (= 13+rpi1),
base-passwd (= 3.6.3),
bash (= 5.2.21-2),
binutils (= 2.41-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
binutils-common (= 2.41-6+rpi1),
bsdextrautils (= 2.39.3-6),
bsdutils (= 1:2.39.3-6),
build-essential (= 12.10),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:13.2.0-1+rpi1),
cpp-12 (= 12.3.0-13+rpi1),
cpp-13 (= 13.2.0-9+rpi1),
dash (= 0.5.12-6),
debconf (= 1.5.82),
debhelper (= 13.11.9),
debianutils (= 5.14),
dh-autoreconf (= 20),
dh-python (= 6.20231223),
dh-strip-nondeterminism (= 1.13.1-1),
diffutils (= 1:3.10-1),
dpkg (= 1.22.1+rpi1),
dpkg-dev (= 1.22.1+rpi1),
dwz (= 0.15-1),
file (= 1:5.45-2),
findutils (= 4.9.0-5),
g++ (= 4:13.2.0-1+rpi1),
g++-13 (= 13.2.0-9+rpi1),
gcc (= 4:13.2.0-1+rpi1),
gcc-12 (= 12.3.0-13+rpi1),
gcc-12-base (= 12.3.0-13+rpi1),
gcc-13 (= 13.2.0-9+rpi1),
gcc-13-base (= 13.2.0-9+rpi1),
gettext (= 0.21-14),
gettext-base (= 0.21-14),
grep (= 3.11-3),
groff-base (= 1.23.0-3),
gzip (= 1.12-1),
hdf5-helpers (= 1.10.10+repack-3),
hostname (= 3.23+nmu1),
init-system-helpers (= 1.66),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-3),
libaec-dev (= 1.1.2-1),
libaec0 (= 1.1.2-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 13.2.0-9+rpi1),
libatomic1 (= 13.2.0-9+rpi1),
libattr1 (= 1:2.5.1-4),
libaudit-common (= 1:3.1.2-1),
libaudit1 (= 1:3.1.2-1),
libbinutils (= 2.41-6+rpi1),
libblkid1 (= 2.39.3-6),
libbrotli1 (= 1.1.0-2),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.37-12+rpi2),
libc-dev-bin (= 2.37-12+rpi2),
libc6 (= 2.37-12+rpi2),
libc6-dev (= 2.37-12+rpi2),
libcap-ng0 (= 0.8.3-3),
libcap2 (= 1:2.66-4),
libcc1-0 (= 13.2.0-9+rpi1),
libcom-err2 (= 1.47.0-2),
libcrypt-dev (= 1:4.4.36-2),
libcrypt1 (= 1:4.4.36-2),
libctf-nobfd0 (= 2.41-6+rpi1),
libctf0 (= 2.41-6+rpi1),
libcurl3-gnutls (= 8.5.0-2+rpi1),
libcurl4 (= 8.5.0-2+rpi1),
libcurl4-gnutls-dev (= 8.5.0-2+rpi1),
libdb5.3 (= 5.3.28+dfsg2-4),
libdebconfclient0 (= 0.271),
libdebhelper-perl (= 13.11.9),
libdeflate-dev (= 1.18-1),
libdeflate0 (= 1.18-1),
libdpkg-perl (= 1.22.1+rpi1),
libeigen3-dev (= 3.4.0-4),
libelf1 (= 0.188-2.1+rpi1),
libexpat1 (= 2.5.0-2),
libfast5-dev (= 0.6.5-7),
libffi8 (= 3.4.4-2),
libfile-find-rule-perl (= 0.34-3),
libfile-stripnondeterminism-perl (= 1.13.1-1),
libgcc-12-dev (= 12.3.0-13+rpi1),
libgcc-13-dev (= 13.2.0-9+rpi1),
libgcc-s1 (= 13.2.0-9+rpi1),
libgcrypt20 (= 1.10.3-2),
libgdbm-compat4 (= 1.23-5),
libgdbm6 (= 1.23-5),
libgfortran5 (= 13.2.0-9+rpi1),
libgmp10 (= 2:6.3.0+dfsg-2),
libgnutls30 (= 3.8.2-1),
libgomp1 (= 13.2.0-9+rpi1),
libgpg-error0 (= 1.47-3),
libgssapi-krb5-2 (= 1.20.1-5),
libhdf5-103-1 (= 1.10.10+repack-3),
libhdf5-cpp-103-1 (= 1.10.10+repack-3),
libhdf5-dev (= 1.10.10+repack-3),
libhdf5-fortran-102 (= 1.10.10+repack-3),
libhdf5-hl-100 (= 1.10.10+repack-3),
libhdf5-hl-cpp-100 (= 1.10.10+repack-3),
libhdf5-hl-fortran-100 (= 1.10.10+repack-3),
libhogweed6 (= 3.9.1-2),
libhts-dev (= 1.18+ds-1),
libhts3 (= 1.18+ds-1),
libhtscodecs2 (= 1.6.0-1),
libicu72 (= 72.1-4),
libidn2-0 (= 2.3.4-1),
libisl23 (= 0.26-3),
libjansson4 (= 2.14-2),
libjpeg-dev (= 1:2.1.5-2),
libjpeg62-turbo (= 1:2.1.5-2),
libjpeg62-turbo-dev (= 1:2.1.5-2),
libk5crypto3 (= 1.20.1-5),
libkeyutils1 (= 1.6.3-2),
libkrb5-3 (= 1.20.1-5),
libkrb5support0 (= 1.20.1-5),
libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
liblz4-1 (= 1.9.4-1+rpi1+b1),
liblzma-dev (= 5.4.5-0.3),
liblzma5 (= 5.4.5-0.3),
libmagic-mgc (= 1:5.45-2),
libmagic1 (= 1:5.45-2),
libmd0 (= 1.1.0-1),
libminimap2-dev (= 2.24+dfsg-3+b1),
libmount1 (= 2.39.3-6),
libmpc3 (= 1.3.1-1),
libmpfr6 (= 4.2.1-1),
libncursesw6 (= 6.4+20231209-1),
libnettle8 (= 3.9.1-2),
libnghttp2-14 (= 1.58.0-1),
libnsl-dev (= 1.3.0-3),
libnsl2 (= 1.3.0-3),
libnumber-compare-perl (= 0.03-3),
libp11-kit0 (= 0.25.3-2),
libpam-modules (= 1.5.2-9.1),
libpam-modules-bin (= 1.5.2-9.1),
libpam-runtime (= 1.5.2-9.1),
libpam0g (= 1.5.2-9.1),
libpcre2-8-0 (= 10.42-4),
libperl5.36 (= 5.36.0-10),
libpipeline1 (= 1.5.7-1),
libpkgconf3 (= 1.8.1-1),
libpsl5 (= 0.21.2-1+b1),
libpython3-stdlib (= 3.11.4-5),
libpython3.11-minimal (= 3.11.7-2),
libpython3.11-stdlib (= 3.11.7-2),
libreadline8 (= 8.2-3),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.28+dfsg1-4),
libsasl2-modules-db (= 2.1.28+dfsg1-4),
libseccomp2 (= 2.5.4-2+rpi1),
libselinux1 (= 3.5-1),
libsframe1 (= 2.41-6+rpi1),
libslow5-0 (= 0.7.0+dfsg-2),
libslow5-dev (= 0.7.0+dfsg-2),
libsmartcols1 (= 2.39.3-6),
libsqlite3-0 (= 3.44.2-1),
libssh2-1 (= 1.11.0-4),
libssl-dev (= 3.1.4-2),
libssl3 (= 3.1.4-2),
libstdc++-13-dev (= 13.2.0-9+rpi1),
libstdc++6 (= 13.2.0-9+rpi1),
libstreamvbyte-dev (= 0.4.1-4),
libstreamvbyte0 (= 0.4.1-4),
libsub-override-perl (= 0.10-1),
libsystemd0 (= 254.5-1+rpi1),
libsz2 (= 1.1.2-1),
libtasn1-6 (= 4.19.0-3),
libtext-glob-perl (= 0.11-3),
libtinfo6 (= 6.4+20231209-1),
libtirpc-common (= 1.3.4+ds-1),
libtirpc-dev (= 1.3.4+ds-1),
libtirpc3 (= 1.3.4+ds-1),
libtool (= 2.4.7-7),
libubsan1 (= 13.2.0-9+rpi1),
libuchardet0 (= 0.0.8-1),
libudev1 (= 254.5-1+rpi1),
libunistring5 (= 1.1-2),
libuuid1 (= 2.39.3-6),
libxml2 (= 2.9.14+dfsg-1.3),
libzstd1 (= 1.5.5+dfsg2-2),
linux-libc-dev (= 6.5.6-1+rpi1),
login (= 1:4.13+dfsg1-3),
m4 (= 1.4.19-4),
make (= 4.3-4.1),
man-db (= 2.12.0-3),
mawk (= 1.3.4.20231126-1),
media-types (= 10.1.0),
ncurses-base (= 6.4+20231209-1),
ncurses-bin (= 6.4+20231209-1),
netbase (= 6.4),
patch (= 2.7.6-7),
perl (= 5.36.0-10),
perl-base (= 5.36.0-10),
perl-modules-5.36 (= 5.36.0-10),
pkg-config (= 1.8.1-1),
pkgconf (= 1.8.1-1),
pkgconf-bin (= 1.8.1-1),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.11.4-5),
python3-distutils (= 3.11.5-1),
python3-lib2to3 (= 3.11.5-1),
python3-minimal (= 3.11.4-5),
python3-pkg-resources (= 68.1.2-2),
python3-setuptools (= 68.1.2-2),
python3.11 (= 3.11.7-2),
python3.11-minimal (= 3.11.7-2),
readline-common (= 8.2-3),
rpcsvc-proto (= 1.4.3-1),
sed (= 4.9-1),
sensible-utils (= 0.0.20),
sysvinit-utils (= 3.08-5),
tar (= 1.34+dfsg-1.3),
tzdata (= 2023c-11),
usr-is-merged (= 38),
usrmerge (= 38),
util-linux (= 2.39.3-6),
xz-utils (= 5.4.5-0.3),
zlib1g (= 1:1.3.dfsg-3),
zlib1g-dev (= 1:1.3.dfsg-3)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
LC_COLLATE="C.UTF-8"
SOURCE_DATE_EPOCH="1705684210"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
nanopolish-dbgsym_0.14.0-1+b2_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 5460328 bytes: control archive=656 bytes.
443 bytes, 12 lines control
302 bytes, 3 lines md5sums
Package: nanopolish-dbgsym
Source: nanopolish (0.14.0-1)
Version: 0.14.0-1+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5723
Depends: nanopolish (= 0.14.0-1+b2)
Section: debug
Priority: optional
Description: debug symbols for nanopolish
Build-Ids: 0cad6fa8f292b34def92faf04c67495719fa1e83 d8fe6436c7c18397d4f76bbfe18e592fe57ed48b
drwxr-xr-x root/root 0 2024-01-19 17:10 ./
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/debug/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/debug/.build-id/0c/
-rw-r--r-- root/root 1779076 2024-01-19 17:10 ./usr/lib/debug/.build-id/0c/ad6fa8f292b34def92faf04c67495719fa1e83.debug
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/debug/.build-id/d8/
-rw-r--r-- root/root 1840920 2024-01-19 17:10 ./usr/lib/debug/.build-id/d8/fe6436c7c18397d4f76bbfe18e592fe57ed48b.debug
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
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nanopolish_0.14.0-1+b2_armhf.deb
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new Debian package, version 2.0.
size 2119084 bytes: control archive=2160 bytes.
981 bytes, 19 lines control
2405 bytes, 31 lines md5sums
305 bytes, 12 lines * postinst #!/bin/sh
380 bytes, 12 lines * prerm #!/bin/sh
Package: nanopolish
Source: nanopolish (0.14.0-1)
Version: 0.14.0-1+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9177
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libhdf5-103-1, libhts3 (>= 1.17), libslow5-0 (>= 0.5.1), libstdc++6 (>= 13.1), 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.
drwxr-xr-x root/root 0 2024-01-19 17:10 ./
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/bin/
-rwxr-xr-x root/root 3791212 2024-01-19 17:10 ./usr/bin/nanopolish
-rwxr-xr-x root/root 75 2022-07-02 09:08 ./usr/bin/nanopolish_makerange
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/nanopolish/
-rwxr-xr-x root/root 2913 2024-01-19 17:10 ./usr/lib/nanopolish/calculate_methylation_frequency.py
-rwxr-xr-x root/root 599 2024-01-19 17:10 ./usr/lib/nanopolish/consensus-preprocess.pl
-rwxr-xr-x root/root 1044 2024-01-19 17:10 ./usr/lib/nanopolish/consensus.make
-rw-r--r-- root/root 923 2024-01-19 17:10 ./usr/lib/nanopolish/convert_all_models.py
-rw-r--r-- root/root 2738 2024-01-19 17:10 ./usr/lib/nanopolish/convert_model_to_header.py
-rw-r--r-- root/root 2090 2024-01-19 17:10 ./usr/lib/nanopolish/dropmodel.py
-rwxr-xr-x root/root 13202 2024-01-19 17:10 ./usr/lib/nanopolish/extract_reads_aligned_to_region.py
-rw-r--r-- root/root 2592 2024-01-19 17:10 ./usr/lib/nanopolish/import_ont_model.py
-rwxr-xr-x root/root 286 2024-01-19 17:10 ./usr/lib/nanopolish/import_ont_models_from_dir.sh
-rwxr-xr-x root/root 1188 2024-01-19 17:10 ./usr/lib/nanopolish/nanopolish_makerange.py
-rw-r--r-- root/root 3136 2024-01-19 17:10 ./usr/lib/nanopolish/nanopolish_merge.py
-rwxr-xr-x root/root 3643692 2024-01-19 17:10 ./usr/lib/nanopolish/nanopolish_test
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/lib/nanopolish/polya_training/
-rw-r--r-- root/root 4915 2024-01-19 17:10 ./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 2024-01-19 17:10 ./usr/lib/nanopolish/polya_training/hmmplot.py
-rw-r--r-- root/root 4071 2024-01-19 17:10 ./usr/lib/nanopolish/polya_training/retrain_emission.py
-rw-r--r-- root/root 4029 2024-01-19 17:10 ./usr/lib/nanopolish/polya_training/workflow.md
-rw-r--r-- root/root 13736 2024-01-19 17:10 ./usr/lib/nanopolish/reestimate_polya_emissions.py
-rw-r--r-- root/root 184 2022-04-19 15:17 ./usr/lib/nanopolish/requirements.txt
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/share/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/share/doc/nanopolish/
-rw-r--r-- root/root 190 2022-07-02 09:08 ./usr/share/doc/nanopolish/README.Debian
-rw-r--r-- root/root 3296 2022-04-19 15:17 ./usr/share/doc/nanopolish/README.md.gz
-rw-r--r-- root/root 278 2022-07-02 09:08 ./usr/share/doc/nanopolish/README.test
-rw-r--r-- root/root 216 2024-01-19 17:10 ./usr/share/doc/nanopolish/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1379 2024-01-19 17:10 ./usr/share/doc/nanopolish/changelog.Debian.gz
-rw-r--r-- root/root 4071 2022-07-02 09:08 ./usr/share/doc/nanopolish/copyright
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/share/doc/nanopolish/examples/
drwxr-xr-x root/root 0 2022-04-19 15:17 ./usr/share/doc/nanopolish/examples/data/
-rw-r--r-- root/root 1850695 2022-04-19 15:17 ./usr/share/doc/nanopolish/examples/data/LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fast5
-rw-r--r-- root/root 487 2022-07-02 09:08 ./usr/share/doc/nanopolish/run-unit-test
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/share/man/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/share/man/man1/
-rw-r--r-- root/root 451 2024-01-19 17:10 ./usr/share/man/man1/nanopolish.1.gz
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/share/python3/
drwxr-xr-x root/root 0 2024-01-19 17:10 ./usr/share/python3/runtime.d/
-rwxr-xr-x root/root 141 2024-01-19 17:10 ./usr/share/python3/runtime.d/nanopolish.rtupdate
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 112036
Build-Time: 104
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 79
Job: nanopolish_0.14.0-1
Machine Architecture: arm64
Package: nanopolish
Package-Time: 196
Source-Version: 0.14.0-1
Space: 112036
Status: successful
Version: 0.14.0-1+b2
--------------------------------------------------------------------------------
Finished at 2024-01-19T17:11:54Z
Build needed 00:03:16, 112036k disk space