I: pbuilder: network access will be disabled during build
I: Current time: Wed Aug 11 01:16:21 +14 2021
I: pbuilder-time-stamp: 1628594181
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/bullseye-reproducible-base.tgz]
I: copying local configuration
I: mounting /proc filesystem
I: mounting /sys filesystem
I: creating /{dev,run}/shm
I: mounting /dev/pts filesystem
I: redirecting /dev/ptmx to /dev/pts/ptmx
I: policy-rc.d already exists
I: Copying source file
I: copying [nanopolish_0.13.2-3.dsc]
I: copying [./nanopolish_0.13.2.orig.tar.gz]
I: copying [./nanopolish_0.13.2-3.debian.tar.xz]
I: Extracting source
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.rHH8IRgx/trustedkeys.kbx': General error
gpgv: Signature made Tue Mar 2 05:45:44 2021 +14
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 nanopolish-0.13.2
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
I: Not using root during the build.
I: Installing the build-deps
I: user script /srv/workspace/pbuilder/30748/tmp/hooks/D01_modify_environment starting
debug: Running on jtx1c.
I: Changing host+domainname to test build reproducibility
I: Adding a custom variable just for the fun of it...
I: Changing /bin/sh to bash
Removing 'diversion of /bin/sh to /bin/sh.distrib by dash'
Adding 'diversion of /bin/sh to /bin/sh.distrib by bash'
Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash'
Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash'
I: Setting pbuilder2's login shell to /bin/bash
I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
I: user script /srv/workspace/pbuilder/30748/tmp/hooks/D01_modify_environment finished
I: user script /srv/workspace/pbuilder/30748/tmp/hooks/D02_print_environment starting
I: set
BASH=/bin/sh
BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath
BASH_ALIASES=()
BASH_ARGC=()
BASH_ARGV=()
BASH_CMDS=()
BASH_LINENO=([0]="12" [1]="0")
BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
BASH_VERSINFO=([0]="5" [1]="1" [2]="4" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf")
BASH_VERSION='5.1.4(1)-release'
BUILDDIR=/build
BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
BUILDUSERNAME=pbuilder2
BUILD_ARCH=armhf
DEBIAN_FRONTEND=noninteractive
DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all,-fixfilepath parallel=4'
DIRSTACK=()
DISTRIBUTION=
EUID=0
FUNCNAME=([0]="Echo" [1]="main")
GROUPS=()
HOME=/root
HOSTNAME=i-capture-the-hostname
HOSTTYPE=arm
HOST_ARCH=armhf
IFS='
'
INVOCATION_ID=53c835a9cd114cd98cd8661d6439cdb3
LANG=C
LANGUAGE=it_CH:it
LC_ALL=C
MACHTYPE=arm-unknown-linux-gnueabihf
MAIL=/var/mail/root
OPTERR=1
OPTIND=1
OSTYPE=linux-gnueabihf
PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
PBCURRENTCOMMANDLINEOPERATION=build
PBUILDER_OPERATION=build
PBUILDER_PKGDATADIR=/usr/share/pbuilder
PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
PBUILDER_SYSCONFDIR=/etc
PIPESTATUS=([0]="0")
POSIXLY_CORRECT=y
PPID=30748
PS4='+ '
PWD=/
SHELL=/bin/bash
SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
SHLVL=3
SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.fwxsM1O87E/pbuilderrc_9VIj --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bullseye-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.fwxsM1O87E/b2 --logfile b2/build.log --extrapackages usrmerge nanopolish_0.13.2-3.dsc'
SUDO_GID=114
SUDO_UID=108
SUDO_USER=jenkins
TERM=unknown
TZ=/usr/share/zoneinfo/Etc/GMT-14
UID=0
USER=root
_='I: set'
http_proxy=http://10.0.0.15:8000/
I: uname -a
Linux i-capture-the-hostname 5.10.0-8-arm64 #1 SMP Debian 5.10.46-4 (2021-08-03) aarch64 GNU/Linux
I: ls -l /bin
total 3580
-rwxr-xr-x 1 root root 816764 Aug 5 10:25 bash
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bunzip2
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bzcat
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzcmp -> bzdiff
-rwxr-xr-x 1 root root 2225 Jul 21 2020 bzdiff
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzegrep -> bzgrep
-rwxr-xr-x 1 root root 4877 Sep 5 2019 bzexe
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzfgrep -> bzgrep
-rwxr-xr-x 1 root root 3775 Jul 21 2020 bzgrep
-rwxr-xr-x 3 root root 26052 Jul 21 2020 bzip2
-rwxr-xr-x 1 root root 9636 Jul 21 2020 bzip2recover
lrwxrwxrwx 1 root root 6 Jul 21 2020 bzless -> bzmore
-rwxr-xr-x 1 root root 1297 Jul 21 2020 bzmore
-rwxr-xr-x 1 root root 26668 Sep 23 2020 cat
-rwxr-xr-x 1 root root 43104 Sep 23 2020 chgrp
-rwxr-xr-x 1 root root 38984 Sep 23 2020 chmod
-rwxr-xr-x 1 root root 43112 Sep 23 2020 chown
-rwxr-xr-x 1 root root 92616 Sep 23 2020 cp
-rwxr-xr-x 1 root root 75524 Dec 11 2020 dash
-rwxr-xr-x 1 root root 75880 Sep 23 2020 date
-rwxr-xr-x 1 root root 55436 Sep 23 2020 dd
-rwxr-xr-x 1 root root 59912 Sep 23 2020 df
-rwxr-xr-x 1 root root 96764 Sep 23 2020 dir
-rwxr-xr-x 1 root root 55012 Jul 29 09:09 dmesg
lrwxrwxrwx 1 root root 8 Nov 8 2019 dnsdomainname -> hostname
lrwxrwxrwx 1 root root 8 Nov 8 2019 domainname -> hostname
-rwxr-xr-x 1 root root 22508 Sep 23 2020 echo
-rwxr-xr-x 1 root root 28 Nov 10 2020 egrep
-rwxr-xr-x 1 root root 22496 Sep 23 2020 false
-rwxr-xr-x 1 root root 28 Nov 10 2020 fgrep
-rwxr-xr-x 1 root root 47492 Jul 29 09:09 findmnt
-rwsr-xr-x 1 root root 26076 Feb 27 06:12 fusermount
-rwxr-xr-x 1 root root 124508 Nov 10 2020 grep
-rwxr-xr-x 2 root root 2346 Mar 3 13:30 gunzip
-rwxr-xr-x 1 root root 6376 Mar 3 13:30 gzexe
-rwxr-xr-x 1 root root 64212 Mar 3 13:30 gzip
-rwxr-xr-x 1 root root 13784 Nov 8 2019 hostname
-rwxr-xr-x 1 root root 43180 Sep 23 2020 ln
-rwxr-xr-x 1 root root 35068 Feb 8 2020 login
-rwxr-xr-x 1 root root 96764 Sep 23 2020 ls
-rwxr-xr-x 1 root root 99940 Jul 29 09:09 lsblk
-rwxr-xr-x 1 root root 51408 Sep 23 2020 mkdir
-rwxr-xr-x 1 root root 43184 Sep 23 2020 mknod
-rwxr-xr-x 1 root root 30780 Sep 23 2020 mktemp
-rwxr-xr-x 1 root root 34408 Jul 29 09:09 more
-rwsr-xr-x 1 root root 34400 Jul 29 09:09 mount
-rwxr-xr-x 1 root root 9824 Jul 29 09:09 mountpoint
-rwxr-xr-x 1 root root 88524 Sep 23 2020 mv
lrwxrwxrwx 1 root root 8 Nov 8 2019 nisdomainname -> hostname
lrwxrwxrwx 1 root root 14 Apr 19 05:38 pidof -> /sbin/killall5
-rwxr-xr-x 1 root root 26652 Sep 23 2020 pwd
lrwxrwxrwx 1 root root 4 Aug 5 10:25 rbash -> bash
-rwxr-xr-x 1 root root 30740 Sep 23 2020 readlink
-rwxr-xr-x 1 root root 43104 Sep 23 2020 rm
-rwxr-xr-x 1 root root 30732 Sep 23 2020 rmdir
-rwxr-xr-x 1 root root 14144 Sep 28 2020 run-parts
-rwxr-xr-x 1 root root 76012 Dec 23 2018 sed
lrwxrwxrwx 1 root root 4 Aug 11 01:16 sh -> bash
lrwxrwxrwx 1 root root 4 Aug 10 23:25 sh.distrib -> dash
-rwxr-xr-x 1 root root 22532 Sep 23 2020 sleep
-rwxr-xr-x 1 root root 55360 Sep 23 2020 stty
-rwsr-xr-x 1 root root 46704 Jul 29 09:09 su
-rwxr-xr-x 1 root root 22532 Sep 23 2020 sync
-rwxr-xr-x 1 root root 340872 Feb 17 23:55 tar
-rwxr-xr-x 1 root root 9808 Sep 28 2020 tempfile
-rwxr-xr-x 1 root root 67696 Sep 23 2020 touch
-rwxr-xr-x 1 root root 22496 Sep 23 2020 true
-rwxr-xr-x 1 root root 9636 Feb 27 06:12 ulockmgr_server
-rwsr-xr-x 1 root root 22108 Jul 29 09:09 umount
-rwxr-xr-x 1 root root 22520 Sep 23 2020 uname
-rwxr-xr-x 2 root root 2346 Mar 3 13:30 uncompress
-rwxr-xr-x 1 root root 96764 Sep 23 2020 vdir
-rwxr-xr-x 1 root root 38512 Jul 29 09:09 wdctl
lrwxrwxrwx 1 root root 8 Nov 8 2019 ypdomainname -> hostname
-rwxr-xr-x 1 root root 1984 Mar 3 13:30 zcat
-rwxr-xr-x 1 root root 1678 Mar 3 13:30 zcmp
-rwxr-xr-x 1 root root 5880 Mar 3 13:30 zdiff
-rwxr-xr-x 1 root root 29 Mar 3 13:30 zegrep
-rwxr-xr-x 1 root root 29 Mar 3 13:30 zfgrep
-rwxr-xr-x 1 root root 2081 Mar 3 13:30 zforce
-rwxr-xr-x 1 root root 7585 Mar 3 13:30 zgrep
-rwxr-xr-x 1 root root 2206 Mar 3 13:30 zless
-rwxr-xr-x 1 root root 1842 Mar 3 13:30 zmore
-rwxr-xr-x 1 root root 4553 Mar 3 13:30 znew
I: user script /srv/workspace/pbuilder/30748/tmp/hooks/D02_print_environment finished
-> Attempting to satisfy build-dependencies
-> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: armhf
Maintainer: Debian Pbuilder Team <pbuilder-maint@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder
This package was created automatically by pbuilder to satisfy the
build-dependencies of the package being currently built.
Depends: debhelper-compat (= 12), dh-python, python3, zlib1g-dev, libfast5-dev (>= 0.6.5), libhts-dev, libeigen3-dev, libminimap2-dev
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 19398 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested:
pbuilder-satisfydepends-dummy depends on debhelper-compat (= 12); however:
Package debhelper-compat is not installed.
pbuilder-satisfydepends-dummy depends on dh-python; however:
Package dh-python is not installed.
pbuilder-satisfydepends-dummy depends on python3; however:
Package python3 is not installed.
pbuilder-satisfydepends-dummy depends on zlib1g-dev; however:
Package zlib1g-dev is not installed.
pbuilder-satisfydepends-dummy depends on libfast5-dev (>= 0.6.5); however:
Package libfast5-dev is not installed.
pbuilder-satisfydepends-dummy depends on libhts-dev; however:
Package libhts-dev is not installed.
pbuilder-satisfydepends-dummy depends on libeigen3-dev; however:
Package libeigen3-dev is not installed.
pbuilder-satisfydepends-dummy depends on libminimap2-dev; however:
Package libminimap2-dev is not installed.
Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0)
The following NEW packages will be installed:
autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} hdf5-helpers{a} intltool-debian{a} libaec-dev{a} libaec0{a} libarchive-zip-perl{a} libbrotli1{a} libcurl3-gnutls{a} libcurl4-gnutls-dev{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libeigen3-dev{a} libelf1{a} libexpat1{a} libfast5-dev{a} libfile-stripnondeterminism-perl{a} libgfortran5{a} libglib2.0-0{a} libhdf5-103-1{a} libhdf5-cpp-103-1{a} libhdf5-dev{a} libhdf5-fortran-102{a} libhdf5-hl-100{a} libhdf5-hl-cpp-100{a} libhdf5-hl-fortran-100{a} libhts-dev{a} libhts3{a} libicu67{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libldap-2.4-2{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libminimap2-dev{a} libmpdec3{a} libnghttp2-14{a} libpipeline1{a} libpsl5{a} libpython3-stdlib{a} libpython3.9-minimal{a} libpython3.9-stdlib{a} libreadline8{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsigsegv2{a} libssh2-1{a} libsub-override-perl{a} libsz2{a} libtool{a} libuchardet0{a} libxml2{a} m4{a} man-db{a} media-types{a} pkg-config{a} po-debconf{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.9{a} python3.9-minimal{a} readline-common{a} sensible-utils{a} zlib1g-dev{a}
The following packages are RECOMMENDED but will NOT be installed:
ca-certificates curl libarchive-cpio-perl libglib2.0-data libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules lynx publicsuffix shared-mime-info wget xdg-user-dirs
0 packages upgraded, 82 newly installed, 0 to remove and 0 not upgraded.
Need to get 36.4 MB of archives. After unpacking 118 MB will be used.
Writing extended state information...
Get: 1 http://deb.debian.org/debian bullseye/main armhf bsdextrautils armhf 2.36.1-8 [138 kB]
Get: 2 http://deb.debian.org/debian bullseye/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get: 3 http://deb.debian.org/debian bullseye/main armhf groff-base armhf 1.22.4-6 [847 kB]
Get: 4 http://deb.debian.org/debian bullseye/main armhf libpipeline1 armhf 1.5.3-1 [30.1 kB]
Get: 5 http://deb.debian.org/debian bullseye/main armhf man-db armhf 2.9.4-2 [1319 kB]
Get: 6 http://deb.debian.org/debian bullseye/main armhf libpython3.9-minimal armhf 3.9.2-1 [790 kB]
Get: 7 http://deb.debian.org/debian bullseye/main armhf libexpat1 armhf 2.2.10-2 [76.3 kB]
Get: 8 http://deb.debian.org/debian bullseye/main armhf python3.9-minimal armhf 3.9.2-1 [1630 kB]
Get: 9 http://deb.debian.org/debian bullseye/main armhf python3-minimal armhf 3.9.2-3 [38.2 kB]
Get: 10 http://deb.debian.org/debian bullseye/main armhf media-types all 4.0.0 [30.3 kB]
Get: 11 http://deb.debian.org/debian bullseye/main armhf libmpdec3 armhf 2.5.1-1 [74.9 kB]
Get: 12 http://deb.debian.org/debian bullseye/main armhf readline-common all 8.1-1 [73.7 kB]
Get: 13 http://deb.debian.org/debian bullseye/main armhf libreadline8 armhf 8.1-1 [147 kB]
Get: 14 http://deb.debian.org/debian bullseye/main armhf libpython3.9-stdlib armhf 3.9.2-1 [1608 kB]
Get: 15 http://deb.debian.org/debian bullseye/main armhf python3.9 armhf 3.9.2-1 [466 kB]
Get: 16 http://deb.debian.org/debian bullseye/main armhf libpython3-stdlib armhf 3.9.2-3 [21.4 kB]
Get: 17 http://deb.debian.org/debian bullseye/main armhf python3 armhf 3.9.2-3 [37.9 kB]
Get: 18 http://deb.debian.org/debian bullseye/main armhf sensible-utils all 0.0.14 [14.8 kB]
Get: 19 http://deb.debian.org/debian bullseye/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get: 20 http://deb.debian.org/debian bullseye/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get: 21 http://deb.debian.org/debian bullseye/main armhf file armhf 1:5.39-3 [68.1 kB]
Get: 22 http://deb.debian.org/debian bullseye/main armhf gettext-base armhf 0.21-4 [171 kB]
Get: 23 http://deb.debian.org/debian bullseye/main armhf libsigsegv2 armhf 2.13-1 [34.0 kB]
Get: 24 http://deb.debian.org/debian bullseye/main armhf m4 armhf 1.4.18-5 [192 kB]
Get: 25 http://deb.debian.org/debian bullseye/main armhf autoconf all 2.69-14 [313 kB]
Get: 26 http://deb.debian.org/debian bullseye/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get: 27 http://deb.debian.org/debian bullseye/main armhf automake all 1:1.16.3-2 [814 kB]
Get: 28 http://deb.debian.org/debian bullseye/main armhf autopoint all 0.21-4 [510 kB]
Get: 29 http://deb.debian.org/debian bullseye/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get: 30 http://deb.debian.org/debian bullseye/main armhf libtool all 2.4.6-15 [513 kB]
Get: 31 http://deb.debian.org/debian bullseye/main armhf dh-autoreconf all 20 [17.1 kB]
Get: 32 http://deb.debian.org/debian bullseye/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get: 33 http://deb.debian.org/debian bullseye/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get: 34 http://deb.debian.org/debian bullseye/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get: 35 http://deb.debian.org/debian bullseye/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get: 36 http://deb.debian.org/debian bullseye/main armhf libelf1 armhf 0.183-1 [161 kB]
Get: 37 http://deb.debian.org/debian bullseye/main armhf dwz armhf 0.13+20210201-1 [179 kB]
Get: 38 http://deb.debian.org/debian bullseye/main armhf libicu67 armhf 67.1-7 [8319 kB]
Get: 39 http://deb.debian.org/debian bullseye/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [602 kB]
Get: 40 http://deb.debian.org/debian bullseye/main armhf gettext armhf 0.21-4 [1243 kB]
Get: 41 http://deb.debian.org/debian bullseye/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get: 42 http://deb.debian.org/debian bullseye/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get: 43 http://deb.debian.org/debian bullseye/main armhf debhelper all 13.3.4 [1049 kB]
Get: 44 http://deb.debian.org/debian bullseye/main armhf python3-lib2to3 all 3.9.2-1 [77.8 kB]
Get: 45 http://deb.debian.org/debian bullseye/main armhf python3-distutils all 3.9.2-1 [143 kB]
Get: 46 http://deb.debian.org/debian bullseye/main armhf dh-python all 4.20201102+nmu1 [99.4 kB]
Get: 47 http://deb.debian.org/debian bullseye/main armhf hdf5-helpers armhf 1.10.6+repack-4 [40.4 kB]
Get: 48 http://deb.debian.org/debian bullseye/main armhf libaec0 armhf 1.0.4-1 [20.4 kB]
Get: 49 http://deb.debian.org/debian bullseye/main armhf libsz2 armhf 1.0.4-1 [6616 B]
Get: 50 http://deb.debian.org/debian bullseye/main armhf libaec-dev armhf 1.0.4-1 [18.3 kB]
Get: 51 http://deb.debian.org/debian bullseye/main armhf libbrotli1 armhf 1.0.9-2+b2 [262 kB]
Get: 52 http://deb.debian.org/debian bullseye/main armhf libsasl2-modules-db armhf 2.1.27+dfsg-2.1 [67.6 kB]
Get: 53 http://deb.debian.org/debian bullseye/main armhf libsasl2-2 armhf 2.1.27+dfsg-2.1 [99.1 kB]
Get: 54 http://deb.debian.org/debian bullseye/main armhf libldap-2.4-2 armhf 2.4.57+dfsg-3 [210 kB]
Get: 55 http://deb.debian.org/debian bullseye/main armhf libnghttp2-14 armhf 1.43.0-1 [65.6 kB]
Get: 56 http://deb.debian.org/debian bullseye/main armhf libpsl5 armhf 0.21.0-1.2 [56.1 kB]
Get: 57 http://deb.debian.org/debian bullseye/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [55.2 kB]
Get: 58 http://deb.debian.org/debian bullseye/main armhf libssh2-1 armhf 1.9.0-2 [143 kB]
Get: 59 http://deb.debian.org/debian bullseye/main armhf libcurl3-gnutls armhf 7.74.0-1.3+b1 [306 kB]
Get: 60 http://deb.debian.org/debian bullseye/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3+b1 [402 kB]
Get: 61 http://deb.debian.org/debian bullseye/main armhf libdeflate0 armhf 1.7-1 [43.1 kB]
Get: 62 http://deb.debian.org/debian bullseye/main armhf libdeflate-dev armhf 1.7-1 [39.9 kB]
Get: 63 http://deb.debian.org/debian bullseye/main armhf libglib2.0-0 armhf 2.66.8-1 [1206 kB]
Get: 64 http://deb.debian.org/debian bullseye/main armhf pkg-config armhf 0.29.2-1 [62.4 kB]
Get: 65 http://deb.debian.org/debian bullseye/main armhf libeigen3-dev all 3.3.9-2 [858 kB]
Get: 66 http://deb.debian.org/debian bullseye/main armhf libhdf5-103-1 armhf 1.10.6+repack-4 [1178 kB]
Get: 67 http://deb.debian.org/debian bullseye/main armhf libgfortran5 armhf 10.2.1-6 [237 kB]
Get: 68 http://deb.debian.org/debian bullseye/main armhf libhdf5-fortran-102 armhf 1.10.6+repack-4 [94.0 kB]
Get: 69 http://deb.debian.org/debian bullseye/main armhf libhdf5-hl-100 armhf 1.10.6+repack-4 [80.5 kB]
Get: 70 http://deb.debian.org/debian bullseye/main armhf libhdf5-hl-fortran-100 armhf 1.10.6+repack-4 [51.2 kB]
Get: 71 http://deb.debian.org/debian bullseye/main armhf libhdf5-cpp-103-1 armhf 1.10.6+repack-4 [133 kB]
Get: 72 http://deb.debian.org/debian bullseye/main armhf libhdf5-hl-cpp-100 armhf 1.10.6+repack-4 [37.4 kB]
Get: 73 http://deb.debian.org/debian bullseye/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [185 kB]
Get: 74 http://deb.debian.org/debian bullseye/main armhf libjpeg62-turbo armhf 1:2.0.6-4 [123 kB]
Get: 75 http://deb.debian.org/debian bullseye/main armhf libjpeg62-turbo-dev armhf 1:2.0.6-4 [242 kB]
Get: 76 http://deb.debian.org/debian bullseye/main armhf libjpeg-dev armhf 1:2.0.6-4 [67.8 kB]
Get: 77 http://deb.debian.org/debian bullseye/main armhf libhdf5-dev armhf 1.10.6+repack-4 [2444 kB]
Get: 78 http://deb.debian.org/debian bullseye/main armhf libfast5-dev all 0.6.5-4 [49.8 kB]
Get: 79 http://deb.debian.org/debian bullseye/main armhf libhts3 armhf 1.11-4 [332 kB]
Get: 80 http://deb.debian.org/debian bullseye/main armhf liblzma-dev armhf 5.2.5-2 [220 kB]
Get: 81 http://deb.debian.org/debian bullseye/main armhf libhts-dev armhf 1.11-4 [3819 kB]
Get: 82 http://deb.debian.org/debian bullseye/main armhf libminimap2-dev armhf 2.17+dfsg-12+b3 [113 kB]
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libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl
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libfile-find-rule-perl libnumber-compare-perl libtext-glob-perl usrmerge
0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded.
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I: Building the package
hostname: Name or service not known
I: Running cd /build/nanopolish-0.13.2/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../nanopolish_0.13.2-3_source.changes
dpkg-buildpackage: info: source package nanopolish
dpkg-buildpackage: info: source version 0.13.2-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --with python3
debian/rules override_dh_auto_clean
make[1]: Entering directory '/build/nanopolish-0.13.2'
sed -i~ 's/^.depend: .*/.depend:/' Makefile
touch .depend
/usr/bin/make clean
make[2]: Entering directory '/build/nanopolish-0.13.2'
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 '/build/nanopolish-0.13.2'
rm -f .depend
mv Makefile~ Makefile
make[1]: Leaving directory '/build/nanopolish-0.13.2'
dh_clean
debian/rules binary
dh binary --with python3
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/build/nanopolish-0.13.2'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/build/nanopolish-0.13.2'
rm -f ./.depend
g++ -o src/main/nanopolish.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/main/nanopolish.cpp
g++ -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -MM src/alignment/nanopolish_alignment_db.cpp src/alignment/nanopolish_anchor.cpp src/alignment/nanopolish_eventalign.cpp src/common/fs_support.cpp src/common/logsum.cpp src/common/nanopolish_alphabet.cpp src/common/nanopolish_bam_processor.cpp src/common/nanopolish_bam_utils.cpp src/common/nanopolish_common.cpp src/common/nanopolish_iupac.cpp src/common/nanopolish_klcs.cpp src/common/nanopolish_variant.cpp src/hmm/nanopolish_duration_model.cpp src/hmm/nanopolish_profile_hmm.cpp src/hmm/nanopolish_profile_hmm_r7.cpp src/hmm/nanopolish_profile_hmm_r9.cpp src/hmm/nanopolish_transition_parameters.cpp src/io/nanopolish_fast5_io.cpp src/io/nanopolish_fast5_loader.cpp src/io/nanopolish_fast5_processor.cpp src/nanopolish_call_methylation.cpp src/nanopolish_call_variants.cpp src/nanopolish_extract.cpp src/nanopolish_getmodel.cpp src/nanopolish_haplotype.cpp src/nanopolish_index.cpp src/nanopolish_methyltrain.cpp src/nanopolish_phase_reads.cpp src/nanopolish_polya_estimator.cpp src/nanopolish_raw_loader.cpp src/nanopolish_read_db.cpp src/nanopolish_scorereads.cpp src/nanopolish_squiggle_read.cpp src/nanopolish_train_poremodel_from_basecalls.cpp src/nanopolish_variant_db.cpp src/nanopolish_vcf2fasta.cpp src/pore_model/nanopolish_model_names.cpp src/pore_model/nanopolish_pore_model_set.cpp src/pore_model/nanopolish_poremodel.cpp src/training_core.cpp src/thirdparty/fet.c src/thirdparty/scrappie/event_detection.c src/thirdparty/scrappie/scrappie_common.c src/thirdparty/stdaln.c > ./.depend;
g++ -o src/alignment/nanopolish_alignment_db.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_alignment_db.cpp
g++ -o src/alignment/nanopolish_anchor.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_anchor.cpp
g++ -o src/alignment/nanopolish_eventalign.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/alignment/nanopolish_eventalign.cpp
g++ -o src/common/fs_support.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/fs_support.cpp
g++ -o src/common/logsum.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/logsum.cpp
g++ -o src/common/nanopolish_alphabet.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_alphabet.cpp
g++ -o src/common/nanopolish_bam_processor.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_bam_processor.cpp
g++ -o src/common/nanopolish_bam_utils.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_bam_utils.cpp
g++ -o src/common/nanopolish_common.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_common.cpp
g++ -o src/common/nanopolish_iupac.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_iupac.cpp
g++ -o src/common/nanopolish_klcs.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_klcs.cpp
g++ -o src/common/nanopolish_variant.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/common/nanopolish_variant.cpp
g++ -o src/hmm/nanopolish_duration_model.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_duration_model.cpp
src/common/nanopolish_variant.cpp: In function 'void score_variant_group(VariantGroup&, Haplotype, const std::vector<HMMInputData>&, int, int, bool, uint32_t, const std::vector<std::__cxx11::basic_string<char> >&)':
src/common/nanopolish_variant.cpp:209:56: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
209 | fprintf(stderr, "Number of variants in span (%lu) would exceed max-haplotypes. Variants may be missed. Consider running with a higher value of max-haplotypes!\n", num_variants);
| ~~^ ~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
g++ -o src/hmm/nanopolish_profile_hmm.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r7.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r7.cpp
g++ -o src/hmm/nanopolish_profile_hmm_r9.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_profile_hmm_r9.cpp
g++ -o src/hmm/nanopolish_transition_parameters.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/hmm/nanopolish_transition_parameters.cpp
g++ -o src/io/nanopolish_fast5_io.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -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
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_loader.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -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
g++ -o src/io/nanopolish_fast5_processor.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/io/nanopolish_fast5_processor.cpp
g++ -o src/nanopolish_call_methylation.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_call_methylation.cpp
g++ -o src/nanopolish_call_variants.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_call_variants.cpp
g++ -o src/nanopolish_extract.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_extract.cpp
g++ -o src/nanopolish_getmodel.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -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_variants.cpp: In function 'Haplotype fix_homopolymers(const Haplotype&, const AlignmentDB&)':
src/nanopolish_call_variants.cpp:680:66: warning: format '%lu' expects argument of type 'long unsigned int', but argument 7 has type 'size_t' {aka 'unsigned int'} [-Wformat=]
680 | fprintf(stderr, "SUM_VAR\t%zu\t%zu\t%d\t%d\t%lu\t%.5lf\t%.2lf\n", ref_hp_start, hp_length, var_sequence_length, call_window, variant_offset_end - variant_offset_start, sum_duration, log_gamma);
| ~~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
| | |
| long unsigned int size_t {aka unsigned int}
| %u
src/nanopolish_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
g++ -o src/nanopolish_haplotype.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_haplotype.cpp
g++ -o src/nanopolish_index.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -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 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_methyltrain.cpp
g++ -o src/nanopolish_phase_reads.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_phase_reads.cpp
g++ -o src/nanopolish_polya_estimator.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_polya_estimator.cpp
g++ -o src/nanopolish_raw_loader.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -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 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_read_db.cpp
g++ -o src/nanopolish_scorereads.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_scorereads.cpp
g++ -o src/nanopolish_squiggle_read.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_squiggle_read.cpp
g++ -o src/nanopolish_train_poremodel_from_basecalls.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_train_poremodel_from_basecalls.cpp
g++ -o src/nanopolish_variant_db.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_variant_db.cpp
g++ -o src/nanopolish_vcf2fasta.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/nanopolish_vcf2fasta.cpp
g++ -o src/pore_model/nanopolish_model_names.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_model_names.cpp
g++ -o src/pore_model/nanopolish_pore_model_set.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_pore_model_set.cpp
g++ -o src/pore_model/nanopolish_poremodel.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/pore_model/nanopolish_poremodel.cpp
g++ -o src/training_core.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/training_core.cpp
cc -o src/thirdparty/fet.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/fet.c
cc -o src/thirdparty/scrappie/event_detection.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/scrappie/event_detection.c
cc -o src/thirdparty/scrappie/scrappie_common.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/scrappie/scrappie_common.c
cc -o src/thirdparty/stdaln.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/thirdparty/stdaln.c
g++ -o nanopolish -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -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 '/build/nanopolish-0.13.2'
dh_auto_test
make -j4 test
make[2]: Entering directory '/build/nanopolish-0.13.2'
g++ -o src/test/nanopolish_test.o -c -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -flto -std=c++11 -fopenmp -fsigned-char -D_FILE_OFFSET_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/hdf5/serial -I/usr/include/eigen3 -I/usr/include/minimap2 -I/usr/include/minimap2 -I./fast5/include -I./src -I./src/hmm -I./src/thirdparty -I./src/thirdparty/scrappie -I./src/common -I./src/alignment -I./src/pore_model -I./src/io -I./eigen/ -fPIC src/test/nanopolish_test.cpp
g++ -o nanopolish_test -g -O2 -fdebug-prefix-map=/build/nanopolish-0.13.2=. -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 '/build/nanopolish-0.13.2'
make[1]: Leaving directory '/build/nanopolish-0.13.2'
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/nanopolish-0.13.2'
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 '/build/nanopolish-0.13.2'
create-stamp debian/debhelper-build-stamp
dh_prep
dh_auto_install
debian/rules override_dh_install
make[1]: Entering directory '/build/nanopolish-0.13.2'
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 '/build/nanopolish-0.13.2'
dh_installdocs
dh_installchangelogs
dh_installexamples
dh_installman
dh_python3
dh_perl
dh_link
dh_strip_nondeterminism
dh_compress
debian/rules override_dh_fixperms
make[1]: Entering directory '/build/nanopolish-0.13.2'
dh_fixperms
find debian -name *.fast5 -exec chmod -x \{\} \;
make[1]: Leaving directory '/build/nanopolish-0.13.2'
dh_missing
dh_dwz
dh_strip
dh_makeshlibs
dh_shlibdeps
dpkg-shlibdeps: warning: debian/nanopolish/usr/lib/nanopolish/nanopolish_test contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
dpkg-shlibdeps: warning: debian/nanopolish/usr/bin/nanopolish contains an unresolvable reference to symbol __aeabi_atexit@GLIBC_2.4: it's probably a plugin
dh_installdeb
dh_gencontrol
dh_md5sums
dh_builddeb
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=binary
dpkg-genchanges --build=binary >../nanopolish_0.13.2-3_armhf.changes
dpkg-genchanges: info: binary-only upload (no source code included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
dpkg-genchanges: info: not including original source code in upload
I: copying local configuration
I: user script /srv/workspace/pbuilder/30748/tmp/hooks/B01_cleanup starting
I: user script /srv/workspace/pbuilder/30748/tmp/hooks/B01_cleanup finished
I: unmounting dev/ptmx filesystem
I: unmounting dev/pts filesystem
I: unmounting dev/shm filesystem
I: unmounting proc filesystem
I: unmounting sys filesystem
I: cleaning the build env
I: removing directory /srv/workspace/pbuilder/30748 and its subdirectories
I: Current time: Wed Aug 11 01:23:27 +14 2021
I: pbuilder-time-stamp: 1628594607