nanopolish →
0.13.2-3 →
armhf → 2021-03-18 18:38:25
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| nanopolish 0.13.2-3 (armhf) Thu, 18 Mar 2021 18:21:57 +0000 |
+==============================================================================+
Package: nanopolish
Version: 0.13.2-3
Source Version: 0.13.2-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-fb44c1c0-76f2-4375-bb5b-99940f6d1538' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/nanopolish-z6IxfZ/resolver-Jkaf7M' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.4 MB in 11s (2259 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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 4078 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main nanopolish 0.13.2-3 (dsc) [2091 B]
Get:2 http://172.17.0.1/private bullseye-staging/main nanopolish 0.13.2-3 (tar) [4067 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main nanopolish 0.13.2-3 (diff) [9248 B]
Fetched 4078 kB in 1s (4976 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/nanopolish-z6IxfZ/nanopolish-0.13.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/nanopolish-z6IxfZ' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 12), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-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 [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [424 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [505 B]
Fetched 1886 B in 0s (48.8 kB/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 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-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3
libicu67 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblzma-dev
libmagic-mgc libmagic1 libminimap2-dev libmpdec3 libnghttp2-14 libpipeline1
libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libsz2 libtool libuchardet0
libxml2 m4 man-db media-types pkg-config po-debconf python3
python3-distutils python3-lib2to3 python3-minimal python3.9
python3.9-minimal sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn11-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev
libeigen3-doc libmpfrc++-dev libhdf5-doc liblzma-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv
python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs publicsuffix libltdl-dev
libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base hdf5-helpers intltool-debian libaec-dev libaec0
libarchive-zip-perl libbrotli1 libcurl3-gnutls libcurl4-gnutls-dev
libdebhelper-perl libdeflate-dev libdeflate0 libeigen3-dev libelf1 libexpat1
libfast5-dev libfile-stripnondeterminism-perl libgfortran5 libglib2.0-0
libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-dev libhdf5-fortran-102
libhdf5-hl-100 libhdf5-hl-cpp-100 libhdf5-hl-fortran-100 libhts-dev libhts3
libicu67 libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev liblzma-dev
libmagic-mgc libmagic1 libminimap2-dev libmpdec3 libnghttp2-14 libpipeline1
libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libsz2 libtool libuchardet0
libxml2 m4 man-db media-types pkg-config po-debconf python3
python3-distutils python3-lib2to3 python3-minimal python3.9
python3.9-minimal sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
0 upgraded, 78 newly installed, 0 to remove and 61 not upgraded.
Need to get 35.3 MB of archives.
After this operation, 123 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [932 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf bsdextrautils armhf 2.36.1-7 [137 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.2-1+rpi1 [791 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-2 [73.4 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.2-1+rpi1 [1625 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.1-1 [37.8 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libmpdec3 armhf 2.5.1-1+rpi1 [73.4 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.2-1+rpi1 [1616 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.2-1+rpi1 [466 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.1-1 [21.0 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.1-1 [64.1 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.14 [14.8 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.183-1 [161 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.4 [1049 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.9.2-1 [77.8 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.9.2-1 [143 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20201102+nmu1 [99.4 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf hdf5-helpers armhf 1.10.6+repack-2 [40.0 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libaec0 armhf 1.0.4-1 [20.0 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libsz2 armhf 1.0.4-1 [6664 B]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libaec-dev armhf 1.0.4-1 [17.8 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.1 [301 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.1 [375 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.7-1 [44.0 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.7-1 [40.3 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.7-2 [1183 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libeigen3-dev all 3.3.9-2 [858 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-103-1 armhf 1.10.6+repack-2 [1184 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-fortran-102 armhf 1.10.6+repack-2 [93.0 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-100 armhf 1.10.6+repack-2 [78.1 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-fortran-100 armhf 1.10.6+repack-2 [49.8 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-cpp-103-1 armhf 1.10.6+repack-2 [128 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-hl-cpp-100 armhf 1.10.6+repack-2 [36.9 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo armhf 1:2.0.6-2 [122 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libjpeg62-turbo-dev armhf 1:2.0.6-2 [240 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libjpeg-dev armhf 1:2.0.6-2 [67.6 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libhdf5-dev armhf 1.10.6+repack-2 [2167 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libfast5-dev all 0.6.5-4 [49.8 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-4 [324 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.5-1.0 [219 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-4 [3815 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libminimap2-dev armhf 2.17+dfsg-12+b1 [110 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 35.3 MB in 8s (4662 kB/s)
Selecting previously unselected package bsdextrautils.
(Reading database ... 12476 files and directories currently installed.)
Preparing to unpack .../0-bsdextrautils_2.36.1-7_armhf.deb ...
Unpacking bsdextrautils (2.36.1-7) ...
Selecting previously unselected package libuchardet0:armhf.
Preparing to unpack .../1-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../2-groff-base_1.22.4-6_armhf.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../3-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../4-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package libpython3.9-minimal:armhf.
Preparing to unpack .../5-libpython3.9-minimal_3.9.2-1+rpi1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.2-1+rpi1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../6-libexpat1_2.2.10-2_armhf.deb ...
Unpacking libexpat1:armhf (2.2.10-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../7-python3.9-minimal_3.9.2-1+rpi1_armhf.deb ...
Unpacking python3.9-minimal (3.9.2-1+rpi1) ...
Setting up libpython3.9-minimal:armhf (3.9.2-1+rpi1) ...
Setting up libexpat1:armhf (2.2.10-2) ...
Setting up python3.9-minimal (3.9.2-1+rpi1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13343 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.9.1-1_armhf.deb ...
Unpacking python3-minimal (3.9.1-1) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../2-libmpdec3_2.5.1-1+rpi1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-1+rpi1) ...
Selecting previously unselected package libpython3.9-stdlib:armhf.
Preparing to unpack .../3-libpython3.9-stdlib_3.9.2-1+rpi1_armhf.deb ...
Unpacking libpython3.9-stdlib:armhf (3.9.2-1+rpi1) ...
Selecting previously unselected package python3.9.
Preparing to unpack .../4-python3.9_3.9.2-1+rpi1_armhf.deb ...
Unpacking python3.9 (3.9.2-1+rpi1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../5-libpython3-stdlib_3.9.1-1_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.9.1-1) ...
Setting up python3-minimal (3.9.1-1) ...
Selecting previously unselected package python3.
(Reading database ... 13740 files and directories currently installed.)
Preparing to unpack .../00-python3_3.9.1-1_armhf.deb ...
Unpacking python3 (3.9.1-1) ...
Selecting previously unselected package sensible-utils.
Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ...
Unpacking sensible-utils (0.0.14) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../02-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../03-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../04-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../05-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../06-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../07-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../08-autoconf_2.69-14_all.deb ...
Unpacking autoconf (2.69-14) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../09-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../10-automake_1%3a1.16.3-2_all.deb ...
Unpacking automake (1:1.16.3-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../11-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../12-libdebhelper-perl_13.3.4_all.deb ...
Unpacking libdebhelper-perl (13.3.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../13-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../14-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../15-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../16-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../17-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../18-dh-strip-nondeterminism_1.11.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.11.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../19-libelf1_0.183-1_armhf.deb ...
Unpacking libelf1:armhf (0.183-1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../20-dwz_0.13+20210201-1_armhf.deb ...
Unpacking dwz (0.13+20210201-1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../21-libicu67_67.1-6_armhf.deb ...
Unpacking libicu67:armhf (67.1-6) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../22-libxml2_2.9.10+dfsg-6.3_armhf.deb ...
Unpacking libxml2:armhf (2.9.10+dfsg-6.3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../23-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../24-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../25-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../26-debhelper_13.3.4_all.deb ...
Unpacking debhelper (13.3.4) ...
Selecting previously unselected package python3-lib2to3.
Preparing to unpack .../27-python3-lib2to3_3.9.2-1_all.deb ...
Unpacking python3-lib2to3 (3.9.2-1) ...
Selecting previously unselected package python3-distutils.
Preparing to unpack .../28-python3-distutils_3.9.2-1_all.deb ...
Unpacking python3-distutils (3.9.2-1) ...
Selecting previously unselected package dh-python.
Preparing to unpack .../29-dh-python_4.20201102+nmu1_all.deb ...
Unpacking dh-python (4.20201102+nmu1) ...
Selecting previously unselected package hdf5-helpers.
Preparing to unpack .../30-hdf5-helpers_1.10.6+repack-2_armhf.deb ...
Unpacking hdf5-helpers (1.10.6+repack-2) ...
Selecting previously unselected package libaec0:armhf.
Preparing to unpack .../31-libaec0_1.0.4-1_armhf.deb ...
Unpacking libaec0:armhf (1.0.4-1) ...
Selecting previously unselected package libsz2:armhf.
Preparing to unpack .../32-libsz2_1.0.4-1_armhf.deb ...
Unpacking libsz2:armhf (1.0.4-1) ...
Selecting previously unselected package libaec-dev:armhf.
Preparing to unpack .../33-libaec-dev_1.0.4-1_armhf.deb ...
Unpacking libaec-dev:armhf (1.0.4-1) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../34-libbrotli1_1.0.9-2+b1_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../35-libnghttp2-14_1.43.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.43.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../36-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../37-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../38-libssh2-1_1.9.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.9.0-2) ...
Selecting previously unselected package libcurl3-gnutls:armhf.
Preparing to unpack .../39-libcurl3-gnutls_7.74.0-1.1_armhf.deb ...
Unpacking libcurl3-gnutls:armhf (7.74.0-1.1) ...
Selecting previously unselected package libcurl4-gnutls-dev:armhf.
Preparing to unpack .../40-libcurl4-gnutls-dev_7.74.0-1.1_armhf.deb ...
Unpacking libcurl4-gnutls-dev:armhf (7.74.0-1.1) ...
Selecting previously unselected package libdeflate0:armhf.
Preparing to unpack .../41-libdeflate0_1.7-1_armhf.deb ...
Unpacking libdeflate0:armhf (1.7-1) ...
Selecting previously unselected package libdeflate-dev:armhf.
Preparing to unpack .../42-libdeflate-dev_1.7-1_armhf.deb ...
Unpacking libdeflate-dev:armhf (1.7-1) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../43-libglib2.0-0_2.66.7-2_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.66.7-2) ...
Selecting previously unselected package pkg-config.
Preparing to unpack .../44-pkg-config_0.29.2-1_armhf.deb ...
Unpacking pkg-config (0.29.2-1) ...
Selecting previously unselected package libeigen3-dev.
Preparing to unpack .../45-libeigen3-dev_3.3.9-2_all.deb ...
Unpacking libeigen3-dev (3.3.9-2) ...
Selecting previously unselected package libhdf5-103-1:armhf.
Preparing to unpack .../46-libhdf5-103-1_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-103-1:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../47-libgfortran5_10.2.1-6+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (10.2.1-6+rpi1) ...
Selecting previously unselected package libhdf5-fortran-102:armhf.
Preparing to unpack .../48-libhdf5-fortran-102_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-fortran-102:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-hl-100:armhf.
Preparing to unpack .../49-libhdf5-hl-100_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-hl-100:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-hl-fortran-100:armhf.
Preparing to unpack .../50-libhdf5-hl-fortran-100_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-hl-fortran-100:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-cpp-103-1:armhf.
Preparing to unpack .../51-libhdf5-cpp-103-1_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-cpp-103-1:armhf (1.10.6+repack-2) ...
Selecting previously unselected package libhdf5-hl-cpp-100:armhf.
Preparing to unpack .../52-libhdf5-hl-cpp-100_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-hl-cpp-100:armhf (1.10.6+repack-2) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../53-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package libjpeg62-turbo:armhf.
Preparing to unpack .../54-libjpeg62-turbo_1%3a2.0.6-2_armhf.deb ...
Unpacking libjpeg62-turbo:armhf (1:2.0.6-2) ...
Selecting previously unselected package libjpeg62-turbo-dev:armhf.
Preparing to unpack .../55-libjpeg62-turbo-dev_1%3a2.0.6-2_armhf.deb ...
Unpacking libjpeg62-turbo-dev:armhf (1:2.0.6-2) ...
Selecting previously unselected package libjpeg-dev:armhf.
Preparing to unpack .../56-libjpeg-dev_1%3a2.0.6-2_armhf.deb ...
Unpacking libjpeg-dev:armhf (1:2.0.6-2) ...
Selecting previously unselected package libhdf5-dev.
Preparing to unpack .../57-libhdf5-dev_1.10.6+repack-2_armhf.deb ...
Unpacking libhdf5-dev (1.10.6+repack-2) ...
Selecting previously unselected package libfast5-dev.
Preparing to unpack .../58-libfast5-dev_0.6.5-4_all.deb ...
Unpacking libfast5-dev (0.6.5-4) ...
Selecting previously unselected package libhts3:armhf.
Preparing to unpack .../59-libhts3_1.11-4_armhf.deb ...
Unpacking libhts3:armhf (1.11-4) ...
Selecting previously unselected package liblzma-dev:armhf.
Preparing to unpack .../60-liblzma-dev_5.2.5-1.0_armhf.deb ...
Unpacking liblzma-dev:armhf (5.2.5-1.0) ...
Selecting previously unselected package libhts-dev:armhf.
Preparing to unpack .../61-libhts-dev_1.11-4_armhf.deb ...
Unpacking libhts-dev:armhf (1.11-4) ...
Selecting previously unselected package libminimap2-dev.
Preparing to unpack .../62-libminimap2-dev_2.17+dfsg-12+b1_armhf.deb ...
Unpacking libminimap2-dev (2.17+dfsg-12+b1) ...
Selecting previously unselected package sbuild-build-depends-main-dummy.
Preparing to unpack .../63-sbuild-build-depends-main-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-main-dummy (0.invalid.0) ...
Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.36.1-7) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up hdf5-helpers (1.10.6+repack-2) ...
Setting up libicu67:armhf (67.1-6) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.66.7-2) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.3.4) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up libdeflate0:armhf (1.7-1) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libaec0:armhf (1.0.4-1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libjpeg62-turbo:armhf (1:2.0.6-2) ...
Setting up libjpeg62-turbo-dev:armhf (1:2.0.6-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up libgfortran5:armhf (10.2.1-6+rpi1) ...
Setting up liblzma-dev:armhf (5.2.5-1.0) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.14) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-1+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.9.0-2) ...
Setting up libdeflate-dev:armhf (1.7-1) ...
Setting up libelf1:armhf (0.183-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libsz2:armhf (1.0.4-1) ...
Setting up libpython3.9-stdlib:armhf (3.9.2-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.11.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up libaec-dev:armhf (1.0.4-1) ...
Setting up libjpeg-dev:armhf (1:2.0.6-2) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.74.0-1.1) ...
Setting up libcurl4-gnutls-dev:armhf (7.74.0-1.1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libminimap2-dev (2.17+dfsg-12+b1) ...
Setting up libeigen3-dev (3.3.9-2) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.11.0-1) ...
Setting up libhdf5-103-1:armhf (1.10.6+repack-2) ...
Setting up dwz (0.13+20210201-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up libhdf5-cpp-103-1:armhf (1.10.6+repack-2) ...
Setting up python3.9 (3.9.2-1+rpi1) ...
Setting up libhdf5-hl-100:armhf (1.10.6+repack-2) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.11-4) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.11-4) ...
Setting up python3 (3.9.1-1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up libhdf5-hl-cpp-100:armhf (1.10.6+repack-2) ...
Setting up libhdf5-fortran-102:armhf (1.10.6+repack-2) ...
Setting up libhdf5-hl-fortran-100:armhf (1.10.6+repack-2) ...
Setting up python3-lib2to3 (3.9.2-1) ...
Setting up python3-distutils (3.9.2-1) ...
Setting up dh-python (4.20201102+nmu1) ...
Setting up debhelper (13.3.4) ...
Setting up libhdf5-dev (1.10.6+repack-2) ...
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 (0.6.5-4) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-9+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.35.1-7+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-9+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.9-1+rpi1
Package versions: adduser_3.118 apt_2.1.18 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1-2 binutils_2.35.1-7+rpi1 binutils-arm-linux-gnueabihf_2.35.1-7+rpi1 binutils-common_2.35.1-7+rpi1 bsdextrautils_2.36.1-7 bsdutils_1:2.36.1-6 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.74 debhelper_13.3.4 debianutils_4.11.2 dh-autoreconf_20 dh-python_4.20201102+nmu1 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.20-1 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.45.7-1 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-6+rpi1 gcc-9-base_9.3.0-20+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-2 hdf5-helpers_1.10.6+repack-2 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libaec-dev_1.0.4-1 libaec0_1.0.4-1 libapt-pkg6.0_2.1.18 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.1-7+rpi1 libblkid1_2.36.1-6 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-9+rpi1 libc-dev-bin_2.31-9+rpi1 libc6_2.31-9+rpi1 libc6-dev_2.31-9+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.45.7-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-7+rpi1 libctf0_2.35.1-7+rpi1 libcurl3-gnutls_7.74.0-1.1 libcurl4-gnutls-dev_7.74.0-1.1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.256 libdebhelper-perl_13.3.4 libdeflate-dev_1.7-1 libdeflate0_1.7-1 libdpkg-perl_1.20.7.1+rpi1 libeigen3-dev_3.3.9-2 libelf1_0.183-1 libexpat1_2.2.10-2 libext2fs2_1.45.7-1 libfakeroot_1.25.3-1.1 libfast5-dev_0.6.5-4 libffi7_3.3-5 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-2 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran5_10.2.1-6+rpi1 libglib2.0-0_2.66.7-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.0-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhdf5-103-1_1.10.6+repack-2 libhdf5-cpp-103-1_1.10.6+repack-2 libhdf5-dev_1.10.6+repack-2 libhdf5-fortran-102_1.10.6+repack-2 libhdf5-hl-100_1.10.6+repack-2 libhdf5-hl-cpp-100_1.10.6+repack-2 libhdf5-hl-fortran-100_1.10.6+repack-2 libhogweed6_3.6-2 libhts-dev_1.11-4 libhts3_1.11-4 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libjpeg-dev_1:2.0.6-2 libjpeg62-turbo_1:2.0.6-2 libjpeg62-turbo-dev_1:2.0.6-2 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-1+rpi1 liblzma-dev_5.2.5-1.0 liblzma5_5.2.5-1.0 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libminimap2-dev_2.17+dfsg-12+b1 libmount1_2.36.1-6 libmpc3_1.2.0-1 libmpdec3_2.5.1-1+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 libnettle8_3.6-2 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libp11-kit0_0.23.22-1 libpam-modules_1.4.0-2 libpam-modules-bin_1.4.0-2 libpam-runtime_1.4.0-2 libpam0g_1.4.0-2 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-2 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.1-1 libpython3.9-minimal_3.9.2-1+rpi1 libpython3.9-stdlib_3.9.2-1+rpi1 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-2+b1 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-6 libsqlite3-0_3.34.1-1 libss2_1.45.7-1 libssh2-1_1.9.0-2 libssl1.1_1.1.1i-3 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.2-5+rpi1 libsz2_1.0.4-1 libtasn1-6_4.16.0-2 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.2-5+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-6 libxml2_2.9.10+dfsg-6.3 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-1 linux-libc-dev_5.10.9-1+rpi1 login_1:4.8.1-1 logsave_1.45.7-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-6 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-2 perl-base_5.32.1-2 perl-modules-5.32_5.32.1-2 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 python3_3.9.1-1 python3-distutils_3.9.2-1 python3-lib2to3_3.9.2-1 python3-minimal_3.9.1-1 python3.9_3.9.2-1+rpi1 python3.9-minimal_3.9.2-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-5 tar_1.32+dfsg-1+rpi1 tzdata_2021a-1 util-linux_2.36.1-6 xz-utils_5.2.5-1.0 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: nanopolish
Binary: nanopolish
Architecture: any
Version: 0.13.2-3
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: 4.5.0
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 (= 12), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev
Package-List:
nanopolish deb science optional arch=any
Checksums-Sha1:
e25b0a8736907a7defa53e32c1671dd7b6a8cc34 4066508 nanopolish_0.13.2.orig.tar.gz
3c732250a8d2ec3132df1adca4bc4ba4b5584d3c 9248 nanopolish_0.13.2-3.debian.tar.xz
Checksums-Sha256:
be9ab70ff0753519323e4cd0e6be50b164c4239bd9c20ffa5207c2d6fc20d120 4066508 nanopolish_0.13.2.orig.tar.gz
cd367dd8a3e0439ef952611b0a07953a3c4e1a6b7b095b136f3baab0b3d69be6 9248 nanopolish_0.13.2-3.debian.tar.xz
Files:
417dcaccd6692d742939454ecde8cc8a 4066508 nanopolish_0.13.2.orig.tar.gz
d90adc42156342fe33ea985d390cfd1d 9248 nanopolish_0.13.2-3.debian.tar.xz
-----BEGIN PGP SIGNATURE-----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=E8RS
-----END PGP SIGNATURE-----
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.ToRER8ms/trustedkeys.kbx': General error
gpgv: Signature made Mon Mar 1 15:45:44 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./nanopolish_0.13.2-3.dsc
dpkg-source: info: extracting nanopolish in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking nanopolish_0.13.2.orig.tar.gz
dpkg-source: info: unpacking nanopolish_0.13.2-3.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 rename_enum.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/build/buildd
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-fb44c1c0-76f2-4375-bb5b-99940f6d1538
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c157543
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package nanopolish
dpkg-buildpackage: info: source version 0.13.2-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
sed -i~ 's/^.depend: .*/.depend:/' Makefile
touch .depend
/usr/bin/make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>'
rm -f nanopolish nanopolish_test src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o \
src/main/nanopolish.o src/test/nanopolish_test.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
rm -f .depend
mv Makefile~ Makefile
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-arch --with python3
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
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 -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/main/nanopolish.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_extract.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend;
g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_alignment_db.cpp
g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_anchor.cpp
g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_eventalign.cpp
g++ -o src/common/fs_support.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/fs_support.cpp
g++ -o src/common/logsum.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/logsum.cpp
g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_alphabet.cpp
g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_bam_processor.cpp
g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_bam_utils.cpp
g++ -o src/common/nanopolish_common.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_common.cpp
g++ -o src/common/nanopolish_iupac.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_iupac.cpp
g++ -o src/common/nanopolish_klcs.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_klcs.cpp
g++ -o src/common/nanopolish_variant.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_variant.cpp
g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_duration_model.cpp
src/common/nanopolish_variant.cpp: In function ‘void score_variant_group(VariantGroup&, Haplotype, const std::vector<HMMInputData>&, int, int, bool, uint32_t, const std::vector<std::__cxx11::basic_string<char> >&)’:
src/common/nanopolish_variant.cpp:209:56: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
209 | fprintf(stderr, "Number of variants in span (%lu) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes!\n", num_variants);
| ~~^ ~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp
g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_transition_parameters.cpp
g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_io.cpp
g++ -o src/io/nanopolish_fast5_loader.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_loader.cpp
src/io/nanopolish_fast5_io.cpp: In function ‘raw_table fast5_get_raw_samples(fast5_file&, const string&, fast5_raw_scaling)’:
src/io/nanopolish_fast5_io.cpp:156:28: warning: narrowing conversion of ‘nsample’ from ‘hsize_t’ {aka ‘long long unsigned int’} to ‘size_t’ {aka ‘unsigned int’} [-Wnarrowing]
156 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
| ^~~~~~~
src/io/nanopolish_fast5_io.cpp:156:40: warning: narrowing conversion of ‘nsample’ from ‘hsize_t’ {aka ‘long long unsigned int’} to ‘size_t’ {aka ‘unsigned int’} [-Wnarrowing]
156 | rawtbl = (raw_table) { nsample, 0, nsample, rawptr };
| ^~~~~~~
g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_processor.cpp
g++ -o src/nanopolish_call_methylation.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_call_methylation.cpp
g++ -o src/nanopolish_call_variants.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_call_variants.cpp
g++ -o src/nanopolish_extract.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_extract.cpp
g++ -o src/nanopolish_getmodel.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_getmodel.cpp
src/nanopolish_call_methylation.cpp: In member function ‘void WatchStatus::update(const string&)’:
src/nanopolish_call_methylation.cpp:120:73: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘double’ [-Wformat=]
120 | fprintf(stderr, "\33[2K\r[call-methylation] fast5 progress: %d/%d %.2lfs/fast5 [%s]", processed_fast5s, seconds_per_file, total_fast5s, message.c_str());
| ~^ ~~~~~~~~~~~~~~~~
| | |
| int double
| %f
src/nanopolish_call_methylation.cpp:120:79: warning: format ‘%lf’ expects argument of type ‘double’, but argument 5 has type ‘int’ [-Wformat=]
120 | fprintf(stderr, "\33[2K\r[call-methylation] fast5 progress: %d/%d %.2lfs/fast5 [%s]", processed_fast5s, seconds_per_file, total_fast5s, message.c_str());
| ~~~~^ ~~~~~~~~~~~~
| | |
| double int
| %.2d
src/nanopolish_call_variants.cpp: In function ‘Haplotype fix_homopolymers(const Haplotype&, const AlignmentDB&)’:
src/nanopolish_call_variants.cpp:680:66: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 7 has type ‘size_t’ {aka ‘unsigned int’} [-Wformat=]
680 | fprintf(stderr, "SUM_VAR\t%zu\t%zu\t%d\t%d\t%lu\t%.5lf\t%.2lf\n", ref_hp_start, hp_length, var_sequence_length, call_window, variant_offset_end - variant_offset_start, sum_duration, log_gamma);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
g++ -o src/nanopolish_haplotype.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_haplotype.cpp
g++ -o src/nanopolish_index.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_index.cpp
src/nanopolish_haplotype.cpp: In member function ‘void Haplotype::print_debug_info() const’:
src/nanopolish_haplotype.cpp:172:61: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘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_methyltrain.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_methyltrain.cpp
g++ -o src/nanopolish_phase_reads.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_phase_reads.cpp
g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_polya_estimator.cpp
g++ -o src/nanopolish_raw_loader.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_raw_loader.cpp
src/nanopolish_polya_estimator.cpp: In function ‘void estimate_polya_for_single_read(const ReadDB&, const faidx_t*, FILE*, const bam_hdr_t*, const bam1_t*, size_t, int, int)’:
src/nanopolish_polya_estimator.cpp:765:40: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘long long int’ [-Wformat=]
765 | fprintf(out_fp, "%s\t%s\t%zu\t-1.0\t-1.0\t-1.0\t-1.0\t-1.00\t-1.00\tREAD_FAILED_LOAD\n",
| ~~^
| |
| unsigned int
| %llu
766 | read_name.c_str(), ref_name.c_str(), record->core.pos);
| ~~~~~~~~~~~~~~~~
| |
| long long int
src/nanopolish_polya_estimator.cpp:823:36: warning: format ‘%zu’ expects argument of type ‘size_t’, but argument 5 has type ‘long long int’ [-Wformat=]
823 | fprintf(out_fp, "%s\t%s\t%zu\t%.1lf\t%.1lf\t%.1lf\t%.1lf\t%.2lf\t%.2lf\t%s\n",
| ~~^
| |
| unsigned int
| %llu
824 | read_name.c_str(), ref_name.c_str(), record->core.pos,
| ~~~~~~~~~~~~~~~~
| |
| long long int
g++ -o src/nanopolish_read_db.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_read_db.cpp
g++ -o src/nanopolish_scorereads.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_scorereads.cpp
g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_squiggle_read.cpp
g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp
g++ -o src/nanopolish_variant_db.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_variant_db.cpp
g++ -o src/nanopolish_vcf2fasta.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_vcf2fasta.cpp
g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_model_names.cpp
g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_pore_model_set.cpp
g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_poremodel.cpp
g++ -o src/training_core.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/training_core.cpp
cc -o src/thirdparty/fet.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/fet.c
cc -o src/thirdparty/scrappie/event_detection.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/scrappie/event_detection.c
cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/scrappie/scrappie_common.c
cc -o src/thirdparty/stdaln.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/stdaln.c
g++ -o nanopolish -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/main/nanopolish.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test
make -j4 test
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -o src/test/nanopolish_test.o -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/test/nanopolish_test.cpp
g++ -o nanopolish_test -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/test/nanopolish_test.o src/alignment/nanopolish_alignment_db.o src/alignment/nanopolish_anchor.o src/alignment/nanopolish_eventalign.o src/common/fs_support.o src/common/logsum.o src/common/nanopolish_alphabet.o src/common/nanopolish_bam_processor.o src/common/nanopolish_bam_utils.o src/common/nanopolish_common.o src/common/nanopolish_iupac.o src/common/nanopolish_klcs.o src/common/nanopolish_variant.o src/hmm/nanopolish_duration_model.o src/hmm/nanopolish_profile_hmm.o src/hmm/nanopolish_profile_hmm_r7.o src/hmm/nanopolish_profile_hmm_r9.o src/hmm/nanopolish_transition_parameters.o src/io/nanopolish_fast5_io.o src/io/nanopolish_fast5_loader.o src/io/nanopolish_fast5_processor.o src/nanopolish_call_methylation.o src/nanopolish_call_variants.o src/nanopolish_extract.o src/nanopolish_getmodel.o src/nanopolish_haplotype.o src/nanopolish_index.o src/nanopolish_methyltrain.o src/nanopolish_phase_reads.o src/nanopolish_polya_estimator.o src/nanopolish_raw_loader.o src/nanopolish_read_db.o src/nanopolish_scorereads.o src/nanopolish_squiggle_read.o src/nanopolish_train_poremodel_from_basecalls.o src/nanopolish_variant_db.o src/nanopolish_vcf2fasta.o src/pore_model/nanopolish_model_names.o src/pore_model/nanopolish_pore_model_set.o src/pore_model/nanopolish_poremodel.o src/training_core.o src/thirdparty/fet.o src/thirdparty/scrappie/event_detection.o src/thirdparty/scrappie/scrappie_common.o src/thirdparty/stdaln.o -lz -lrt -lhdf5 -lhts -lminimap2 -Wl,-z,relro -Wl,-z,now -L/usr/lib/arm-linux-gnueabihf/hdf5/serial
./nanopolish_test
===============================================================================
All tests passed (636 assertions in 6 test cases)
make[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 createt inside build time test in autopkgtest this is enforced in dh_auto_build to circumvent nocheck."
Since we need the executable createt 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 -a
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
for pl in `find debian -name "*.pl"` ; do \
sed -i '1s?^#!/usr/bin/env.*perl?#!/usr/bin/perl?' ${pl} ; \
done
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env *python' debian/*/usr/*` ; do \
sed -i '1s?^#!.*python.*?#!/usr/bin/python3?' ${pl} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_python3 -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian -name *.fast5 -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/nanopolish/usr/bin/nanopolish contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
dpkg-shlibdeps: warning: debian/nanopolish/usr/lib/nanopolish/nanopolish_test contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'nanopolish-dbgsym' in '../nanopolish-dbgsym_0.13.2-3_armhf.deb'.
dpkg-deb: building package 'nanopolish' in '../nanopolish_0.13.2-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../nanopolish_0.13.2-3_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 2021-03-18T18:38:16Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
nanopolish_0.13.2-3_armhf.changes:
----------------------------------
Format: 1.8
Date: Mon, 01 Mar 2021 16:39:39 +0100
Source: nanopolish
Binary: nanopolish nanopolish-dbgsym
Architecture: armhf
Version: 0.13.2-3
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
nanopolish - consensus caller for nanopore sequencing data
Closes: 983767
Changes:
nanopolish (0.13.2-3) unstable; urgency=medium
.
* Since we need the executable createt inside build time test in autopkgtest
this is enforced in dh_auto_build to circumvent nocheck.
Closes: #983767
Checksums-Sha1:
42129d27bc42c48507138c6b6da65e56d1582bb4 8021644 nanopolish-dbgsym_0.13.2-3_armhf.deb
70a562e30270a05badf7109769f2b7eafbfe1b82 6713 nanopolish_0.13.2-3_armhf.buildinfo
f292e9340d7636cec58f65a5a9dc4ff3a1f8c5aa 2173596 nanopolish_0.13.2-3_armhf.deb
Checksums-Sha256:
236b27c71b1d86f6b7ed9fef351a773cf6a3c32281229175bfa4bb630617cbab 8021644 nanopolish-dbgsym_0.13.2-3_armhf.deb
5ff7561628bcba82a595e72cabbe4e3abc6676e0b6c5d0a14d6c51495b1d5297 6713 nanopolish_0.13.2-3_armhf.buildinfo
988ec5b6f541036b63b4f2bb34652e0f867cce745ff404e4ce7594952b13e081 2173596 nanopolish_0.13.2-3_armhf.deb
Files:
f769b967e968bf0549be43afd39e269c 8021644 debug optional nanopolish-dbgsym_0.13.2-3_armhf.deb
ad7585f43bfe8606e0abf4ef6b7f107d 6713 science optional nanopolish_0.13.2-3_armhf.buildinfo
c21cde51540ebad9b9e0f0720123ae06 2173596 science optional nanopolish_0.13.2-3_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: nanopolish
Binary: nanopolish nanopolish-dbgsym
Architecture: armhf
Version: 0.13.2-3
Checksums-Md5:
f769b967e968bf0549be43afd39e269c 8021644 nanopolish-dbgsym_0.13.2-3_armhf.deb
c21cde51540ebad9b9e0f0720123ae06 2173596 nanopolish_0.13.2-3_armhf.deb
Checksums-Sha1:
42129d27bc42c48507138c6b6da65e56d1582bb4 8021644 nanopolish-dbgsym_0.13.2-3_armhf.deb
f292e9340d7636cec58f65a5a9dc4ff3a1f8c5aa 2173596 nanopolish_0.13.2-3_armhf.deb
Checksums-Sha256:
236b27c71b1d86f6b7ed9fef351a773cf6a3c32281229175bfa4bb630617cbab 8021644 nanopolish-dbgsym_0.13.2-3_armhf.deb
988ec5b6f541036b63b4f2bb34652e0f867cce745ff404e4ce7594952b13e081 2173596 nanopolish_0.13.2-3_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Thu, 18 Mar 2021 18:38:14 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.69-14),
automake (= 1:1.16.3-2),
autopoint (= 0.21-4),
autotools-dev (= 20180224.1+nmu1),
base-files (= 11+rpi1),
base-passwd (= 3.5.48),
bash (= 5.1-2),
binutils (= 2.35.1-7+rpi1),
binutils-arm-linux-gnueabihf (= 2.35.1-7+rpi1),
binutils-common (= 2.35.1-7+rpi1),
bsdextrautils (= 2.36.1-7),
bsdutils (= 1:2.36.1-6),
build-essential (= 12.9),
bzip2 (= 1.0.8-4),
coreutils (= 8.32-4),
cpp (= 4:10.2.1-1+rpi1),
cpp-10 (= 10.2.1-6+rpi1),
dash (= 0.5.11+git20200708+dd9ef66-5),
debconf (= 1.5.74),
debhelper (= 13.3.4),
debianutils (= 4.11.2),
dh-autoreconf (= 20),
dh-python (= 4.20201102+nmu1),
dh-strip-nondeterminism (= 1.11.0-1),
diffutils (= 1:3.7-5),
dpkg (= 1.20.7.1+rpi1),
dpkg-dev (= 1.20.7.1+rpi1),
dwz (= 0.13+20210201-1),
file (= 1:5.39-3),
findutils (= 4.8.0-1),
g++ (= 4:10.2.1-1+rpi1),
g++-10 (= 10.2.1-6+rpi1),
gcc (= 4:10.2.1-1+rpi1),
gcc-10 (= 10.2.1-6+rpi1),
gcc-10-base (= 10.2.1-6+rpi1),
gettext (= 0.21-4),
gettext-base (= 0.21-4),
grep (= 3.6-1),
groff-base (= 1.22.4-6),
gzip (= 1.10-2),
hdf5-helpers (= 1.10.6+repack-2),
hostname (= 3.23),
init-system-helpers (= 1.60),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.2.53-10),
libaec-dev (= 1.0.4-1),
libaec0 (= 1.0.4-1),
libarchive-zip-perl (= 1.68-1),
libasan6 (= 10.2.1-6+rpi1),
libatomic1 (= 10.2.1-6+rpi1),
libattr1 (= 1:2.4.48-6),
libaudit-common (= 1:3.0-2),
libaudit1 (= 1:3.0-2),
libbinutils (= 2.35.1-7+rpi1),
libblkid1 (= 2.36.1-6),
libbrotli1 (= 1.0.9-2+b1),
libbz2-1.0 (= 1.0.8-4),
libc-bin (= 2.31-9+rpi1),
libc-dev-bin (= 2.31-9+rpi1),
libc6 (= 2.31-9+rpi1),
libc6-dev (= 2.31-9+rpi1),
libcap-ng0 (= 0.7.9-2.2+b1),
libcc1-0 (= 10.2.1-6+rpi1),
libcom-err2 (= 1.45.7-1),
libcrypt-dev (= 1:4.4.17-1),
libcrypt1 (= 1:4.4.17-1),
libctf-nobfd0 (= 2.35.1-7+rpi1),
libctf0 (= 2.35.1-7+rpi1),
libcurl3-gnutls (= 7.74.0-1.1),
libcurl4-gnutls-dev (= 7.74.0-1.1),
libdb5.3 (= 5.3.28+dfsg1-0.6),
libdebconfclient0 (= 0.256),
libdebhelper-perl (= 13.3.4),
libdeflate-dev (= 1.7-1),
libdeflate0 (= 1.7-1),
libdpkg-perl (= 1.20.7.1+rpi1),
libeigen3-dev (= 3.3.9-2),
libelf1 (= 0.183-1),
libexpat1 (= 2.2.10-2),
libfast5-dev (= 0.6.5-4),
libffi7 (= 3.3-5),
libfile-stripnondeterminism-perl (= 1.11.0-1),
libgcc-10-dev (= 10.2.1-6+rpi1),
libgcc-s1 (= 10.2.1-6+rpi1),
libgcrypt20 (= 1.8.7-2),
libgdbm-compat4 (= 1.19-2),
libgdbm6 (= 1.19-2),
libgfortran5 (= 10.2.1-6+rpi1),
libglib2.0-0 (= 2.66.7-2),
libgmp10 (= 2:6.2.1+dfsg-1),
libgnutls30 (= 3.7.0-5),
libgomp1 (= 10.2.1-6+rpi1),
libgpg-error0 (= 1.38-2),
libgssapi-krb5-2 (= 1.18.3-4),
libhdf5-103-1 (= 1.10.6+repack-2),
libhdf5-cpp-103-1 (= 1.10.6+repack-2),
libhdf5-dev (= 1.10.6+repack-2),
libhdf5-fortran-102 (= 1.10.6+repack-2),
libhdf5-hl-100 (= 1.10.6+repack-2),
libhdf5-hl-cpp-100 (= 1.10.6+repack-2),
libhdf5-hl-fortran-100 (= 1.10.6+repack-2),
libhogweed6 (= 3.6-2),
libhts-dev (= 1.11-4),
libhts3 (= 1.11-4),
libicu67 (= 67.1-6),
libidn2-0 (= 2.3.0-5),
libisl23 (= 0.23-1),
libjpeg-dev (= 1:2.0.6-2),
libjpeg62-turbo (= 1:2.0.6-2),
libjpeg62-turbo-dev (= 1:2.0.6-2),
libk5crypto3 (= 1.18.3-4),
libkeyutils1 (= 1.6.1-2),
libkrb5-3 (= 1.18.3-4),
libkrb5support0 (= 1.18.3-4),
libldap-2.4-2 (= 2.4.57+dfsg-1),
liblz4-1 (= 1.9.3-1+rpi1),
liblzma-dev (= 5.2.5-1.0),
liblzma5 (= 5.2.5-1.0),
libmagic-mgc (= 1:5.39-3),
libmagic1 (= 1:5.39-3),
libminimap2-dev (= 2.17+dfsg-12+b1),
libmount1 (= 2.36.1-6),
libmpc3 (= 1.2.0-1),
libmpdec3 (= 2.5.1-1+rpi1),
libmpfr6 (= 4.1.0-3),
libncursesw6 (= 6.2+20201114-2),
libnettle8 (= 3.6-2),
libnghttp2-14 (= 1.43.0-1),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libp11-kit0 (= 0.23.22-1),
libpam-modules (= 1.4.0-2),
libpam-modules-bin (= 1.4.0-2),
libpam-runtime (= 1.4.0-2),
libpam0g (= 1.4.0-2),
libpcre2-8-0 (= 10.36-2),
libpcre3 (= 2:8.39-13),
libperl5.32 (= 5.32.1-2),
libpipeline1 (= 1.5.3-1),
libpsl5 (= 0.21.0-1.2),
libpython3-stdlib (= 3.9.1-1),
libpython3.9-minimal (= 3.9.2-1+rpi1),
libpython3.9-stdlib (= 3.9.2-1+rpi1),
libreadline8 (= 8.1-1),
librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
libsasl2-2 (= 2.1.27+dfsg-2),
libsasl2-modules-db (= 2.1.27+dfsg-2),
libseccomp2 (= 2.5.1-1+rpi1),
libselinux1 (= 3.1-2+b1),
libsigsegv2 (= 2.13-1),
libsmartcols1 (= 2.36.1-6),
libsqlite3-0 (= 3.34.1-1),
libssh2-1 (= 1.9.0-2),
libssl1.1 (= 1.1.1i-3),
libstdc++-10-dev (= 10.2.1-6+rpi1),
libstdc++6 (= 10.2.1-6+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 247.2-5+rpi1),
libsz2 (= 1.0.4-1),
libtasn1-6 (= 4.16.0-2),
libtinfo6 (= 6.2+20201114-2),
libtirpc-common (= 1.3.1-1),
libtirpc-dev (= 1.3.1-1),
libtirpc3 (= 1.3.1-1),
libtool (= 2.4.6-15),
libubsan1 (= 10.2.1-6+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 247.2-5+rpi1),
libunistring2 (= 0.9.10-4),
libuuid1 (= 2.36.1-6),
libxml2 (= 2.9.10+dfsg-6.3),
libzstd1 (= 1.4.8+dfsg-1),
linux-libc-dev (= 5.10.9-1+rpi1),
login (= 1:4.8.1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-5),
make (= 4.3-4),
man-db (= 2.9.4-2),
mawk (= 1.3.4.20200120-2),
media-types (= 4.0.0),
ncurses-base (= 6.2+20201114-2),
ncurses-bin (= 6.2+20201114-2),
patch (= 2.7.6-7),
perl (= 5.32.1-2),
perl-base (= 5.32.1-2),
perl-modules-5.32 (= 5.32.1-2),
pkg-config (= 0.29.2-1),
po-debconf (= 1.0.21+nmu1),
python3 (= 3.9.1-1),
python3-distutils (= 3.9.2-1),
python3-lib2to3 (= 3.9.2-1),
python3-minimal (= 3.9.1-1),
python3.9 (= 3.9.2-1+rpi1),
python3.9-minimal (= 3.9.2-1+rpi1),
readline-common (= 8.1-1),
sed (= 4.7-1),
sensible-utils (= 0.0.14),
sysvinit-utils (= 2.96-5),
tar (= 1.32+dfsg-1+rpi1),
tzdata (= 2021a-1),
util-linux (= 2.36.1-6),
xz-utils (= 5.2.5-1.0),
zlib1g (= 1:1.2.11.dfsg-2),
zlib1g-dev (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1614613179"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
nanopolish-dbgsym_0.13.2-3_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 8021644 bytes: control archive=648 bytes.
426 bytes, 12 lines control
302 bytes, 3 lines md5sums
Package: nanopolish-dbgsym
Source: nanopolish
Version: 0.13.2-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8395
Depends: nanopolish (= 0.13.2-3)
Section: debug
Priority: optional
Description: debug symbols for nanopolish
Build-Ids: 3f570cb0150d512320d45c66f94a24704f0c687c b70ffa1fee903f76a1f096164d12e09a92e12411
drwxr-xr-x root/root 0 2021-03-01 15:39 ./
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/debug/.build-id/3f/
-rw-r--r-- root/root 2877636 2021-03-01 15:39 ./usr/lib/debug/.build-id/3f/570cb0150d512320d45c66f94a24704f0c687c.debug
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/debug/.build-id/b7/
-rw-r--r-- root/root 2566332 2021-03-01 15:39 ./usr/lib/debug/.build-id/b7/0ffa1fee903f76a1f096164d12e09a92e12411.debug
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 3137344 2021-03-01 15:39 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/nanopolish.debug
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-03-01 15:39 ./usr/share/doc/nanopolish-dbgsym -> nanopolish
nanopolish_0.13.2-3_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 2173596 bytes: control archive=2120 bytes.
894 bytes, 18 lines control
2320 bytes, 30 lines md5sums
283 bytes, 12 lines * postinst #!/bin/sh
394 bytes, 12 lines * prerm #!/bin/sh
Package: nanopolish
Version: 0.13.2-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9357
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libhdf5-103-1, libhts3 (>= 1.10), libstdc++6 (>= 9), zlib1g (>= 1:1.1.4), python3:any, perl:any
Recommends: python3-biopython, python3-pysam
Suggests: perl, make
Section: science
Priority: optional
Homepage: https://github.com/jts/nanopolish
Description: consensus caller for nanopore sequencing data
Nanopolish uses a signal-level hidden Markov model for consensus calling
of nanopore genome sequencing data. It can perform signal-level analysis
of Oxford Nanopore sequencing data. Nanopolish can calculate an improved
consensus sequence for a draft genome assembly, detect base
modifications, call SNPs and indels with respect to a reference genome
and more.
drwxr-xr-x root/root 0 2021-03-01 15:39 ./
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/bin/
-rwxr-xr-x root/root 3959140 2021-03-01 15:39 ./usr/bin/nanopolish
-rwxr-xr-x root/root 75 2021-03-01 15:39 ./usr/bin/nanopolish_makerange
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/nanopolish/
-rwxr-xr-x root/root 2913 2021-03-01 15:39 ./usr/lib/nanopolish/calculate_methylation_frequency.py
-rwxr-xr-x root/root 599 2021-03-01 15:39 ./usr/lib/nanopolish/consensus-preprocess.pl
-rwxr-xr-x root/root 1044 2021-03-01 15:39 ./usr/lib/nanopolish/consensus.make
-rw-r--r-- root/root 923 2021-03-01 15:39 ./usr/lib/nanopolish/convert_all_models.py
-rw-r--r-- root/root 2738 2021-03-01 15:39 ./usr/lib/nanopolish/convert_model_to_header.py
-rw-r--r-- root/root 2090 2021-03-01 15:39 ./usr/lib/nanopolish/dropmodel.py
-rwxr-xr-x root/root 13202 2021-03-01 15:39 ./usr/lib/nanopolish/extract_reads_aligned_to_region.py
-rw-r--r-- root/root 2592 2021-03-01 15:39 ./usr/lib/nanopolish/import_ont_model.py
-rwxr-xr-x root/root 286 2021-03-01 15:39 ./usr/lib/nanopolish/import_ont_models_from_dir.sh
-rwxr-xr-x root/root 1188 2021-03-01 15:39 ./usr/lib/nanopolish/nanopolish_makerange.py
-rw-r--r-- root/root 3136 2021-03-01 15:39 ./usr/lib/nanopolish/nanopolish_merge.py
-rwxr-xr-x root/root 3660028 2021-03-01 15:39 ./usr/lib/nanopolish/nanopolish_test
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/lib/nanopolish/polya_training/
-rw-r--r-- root/root 4915 2021-03-01 15:39 ./usr/lib/nanopolish/polya_training/dump_signal.py
-rw-r--r-- root/root 2248 2020-04-23 18:43 ./usr/lib/nanopolish/polya_training/environment.yml
-rw-r--r-- root/root 4739 2021-03-01 15:39 ./usr/lib/nanopolish/polya_training/hmmplot.py
-rw-r--r-- root/root 4071 2021-03-01 15:39 ./usr/lib/nanopolish/polya_training/retrain_emission.py
-rw-r--r-- root/root 4029 2021-03-01 15:39 ./usr/lib/nanopolish/polya_training/workflow.md
-rw-r--r-- root/root 13736 2021-03-01 15:39 ./usr/lib/nanopolish/reestimate_polya_emissions.py
-rw-r--r-- root/root 184 2020-04-23 18:43 ./usr/lib/nanopolish/requirements.txt
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/doc/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/doc/nanopolish/
-rw-r--r-- root/root 190 2021-03-01 15:39 ./usr/share/doc/nanopolish/README.Debian
-rw-r--r-- root/root 3202 2020-04-23 18:43 ./usr/share/doc/nanopolish/README.md.gz
-rw-r--r-- root/root 278 2021-03-01 15:39 ./usr/share/doc/nanopolish/README.test
-rw-r--r-- root/root 2388 2021-03-01 15:39 ./usr/share/doc/nanopolish/changelog.Debian.gz
-rw-r--r-- root/root 4071 2021-03-01 15:39 ./usr/share/doc/nanopolish/copyright
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/doc/nanopolish/examples/
drwxr-xr-x root/root 0 2020-04-23 18:43 ./usr/share/doc/nanopolish/examples/data/
-rw-r--r-- root/root 1850695 2020-04-23 18:43 ./usr/share/doc/nanopolish/examples/data/LomanLabz_PC_Ecoli_K12_R7.3_2549_1_ch8_file30_strand.fast5
-rw-r--r-- root/root 487 2021-03-01 15:39 ./usr/share/doc/nanopolish/run-unit-test
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/man/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/man/man1/
-rw-r--r-- root/root 329 2021-03-01 15:39 ./usr/share/man/man1/nanopolish.1.gz
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/python3/
drwxr-xr-x root/root 0 2021-03-01 15:39 ./usr/share/python3/runtime.d/
-rwxr-xr-x root/root 141 2021-03-01 15:39 ./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: 160800
Build-Time: 562
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 388
Job: nanopolish_0.13.2-3
Machine Architecture: armhf
Package: nanopolish
Package-Time: 979
Source-Version: 0.13.2-3
Space: 160800
Status: successful
Version: 0.13.2-3
--------------------------------------------------------------------------------
Finished at 2021-03-18T18:38:16Z
Build needed 00:16:19, 160800k disk space