Raspbian Package Auto-Building

Build log for ivar (1.2.2+dfsg-2) on armhf

ivar1.2.2+dfsg-2armhf → 2020-06-05 02:16:34

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02

+==============================================================================+
| ivar 1.2.2+dfsg-2 (armhf)                    Fri, 05 Jun 2020 02:13:06 +0000 |
+==============================================================================+

Package: ivar
Version: 1.2.2+dfsg-2
Source Version: 1.2.2+dfsg-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-bb7fcc45-fa18-4452-a49e-fa1d29dca59c' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 9s (2683 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'ivar' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/ivar.git
Please use:
git clone https://salsa.debian.org/med-team/ivar.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 627 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main ivar 1.2.2+dfsg-2 (dsc) [1991 B]
Get:2 http://172.17.0.1/private bullseye-staging/main ivar 1.2.2+dfsg-2 (tar) [621 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main ivar 1.2.2+dfsg-2 (diff) [3940 B]
Fetched 627 kB in 0s (3316 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/ivar-4CIWQB/ivar-1.2.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ivar-4CIWQB' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install build-essential                                                      |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-aspSJ1/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-aspSJ1/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-aspSJ1/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg:               imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (8307 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 33 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (53.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12233 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), libhts-dev
Filtered Build-Depends: debhelper-compat (= 13), libhts-dev
dpkg-deb: building package 'sbuild-build-depends-ivar-dummy' in '/<<BUILDDIR>>/resolver-aspSJ1/apt_archive/sbuild-build-depends-ivar-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-ivar-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ Sources [494 B]
Get:5 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ Packages [575 B]
Fetched 2402 B in 0s (9238 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

Install ivar build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcroco3
  libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
  libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
  libhts3 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
  librtmp1 libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtinfo5
  libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
  krb5-user liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
  m4-doc apparmor less www-browser libmail-box-perl
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl libglib2.0-data
  shared-mime-info xdg-user-dirs krb5-locales publicsuffix libltdl-dev
  libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libcroco3
  libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
  libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
  libhts3 libicu63 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0
  liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
  librtmp1 libsigsegv2 libssh2-1 libssl1.1 libsub-override-perl libtinfo5
  libtool libuchardet0 libxml2 m4 man-db po-debconf
  sbuild-build-depends-ivar-dummy sensible-utils zlib1g-dev
0 upgraded, 53 newly installed, 0 to remove and 33 not upgraded.
Need to get 27.0 MB of archives.
After this operation, 82.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-aspSJ1/apt_archive ./ sbuild-build-depends-ivar-dummy 0.invalid.0 [860 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.1 [187 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.1-1 [14.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.3-1 [1159 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5 [592 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.1 [1012 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7+rpi1 [61.5 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7+rpi1 [112 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1g-1 [1272 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7+rpi1 [318 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7+rpi1 [135 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1 [53.9 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.68.0-1 [284 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-3 [319 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-3 [4796 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 27.0 MB in 4s (6118 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 12233 files and directories currently installed.)
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Unpacking libbsd0:armhf (0.10.0-1) ...
Selecting previously unselected package libtinfo5:armhf.
Preparing to unpack .../01-libtinfo5_6.2-1_armhf.deb ...
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Preparing to unpack .../04-groff-base_1.22.4-5_armhf.deb ...
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Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.3-1) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1g-1) ...
Setting up libdebhelper-perl (13.1) ...
Setting up libbrotli1:armhf (1.0.7-6.1) ...
Setting up libnghttp2-14:armhf (1.40.0-1+b2) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up libdeflate0:armhf (1.6-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-5) ...
Setting up libicu63:armhf (63.2-3) ...
Setting up libkrb5support0:armhf (1.17-7+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up libk5crypto3:armhf (1.17-7+rpi1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-7+rpi1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (1.8.1-1) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-7+rpi1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11.1) ...
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Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
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Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhts3:armhf (1.10.2-3) ...
Setting up po-debconf (1.0.21) ...
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Setting up dh-autoreconf (19) ...
Setting up debhelper (13.1) ...
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Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.15.0-76-generic armhf (armv8l)
Toolchain package versions: binutils_2.34-8+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-12+rpi1 gcc-9_9.3.0-12+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-12+rpi1 libstdc++6_10.1.0-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.4 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-8+rpi1 binutils-arm-linux-gnueabihf_2.34-8+rpi1 binutils-common_2.34-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.35.1-5 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-12+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-5 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-12+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-1+rpi1 gcc-9_9.3.0-12+rpi1 gcc-9-base_9.3.0-12+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.4 libarchive-zip-perl_1.68-1 libasan5_9.3.0-12+rpi1 libassuan0_2.5.3-7 libatomic1_10.1.0-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-8+rpi1 libblkid1_2.35.1-5 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.1+b1 libcap2_1:2.34-2 libcap2-bin_1:2.34-2 libcc1-0_10.1.0-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-8+rpi1 libctf0_2.34-8+rpi1 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.252 libdebhelper-perl_13.1 libdeflate0_1.6-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.35.1-5 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-12+rpi1 libgcc-s1_10.1.0-1+rpi1 libgcc1_1:10.1.0-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.3-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10.1.0-1+rpi1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7+rpi1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-7+rpi1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7+rpi1 libkrb5support0_1.17-7+rpi1 libksba8_1.3.5-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.1-5 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.34-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpsl5_0.21.0-1 libreadline7_7.0-5 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-12+rpi1 libstdc++6_10.1.0-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.5-3+rpi1 libtasn1-6_4.16.0-2 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-1+rpi1 libuchardet0_0.0.6-3 libudev1_245.5-3+rpi1 libunistring2_0.9.10-2 libuuid1_2.35.1-5 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mount_2.35.1-5 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ivar-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.1-5 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed May 27 11:25:54 2020 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 ./ivar_1.2.2+dfsg-2.dsc
dpkg-source: info: extracting ivar in /<<BUILDDIR>>/ivar-1.2.2+dfsg
dpkg-source: info: unpacking ivar_1.2.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking ivar_1.2.2+dfsg-2.debian.tar.xz

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-bb7fcc45-fa18-4452-a49e-fa1d29dca59c
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: info: source package ivar
dpkg-buildpackage: info: source version 1.2.2+dfsg-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
configure.ac:12: installing './compile'
configure.ac:6: installing './install-sh'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
   dh_auto_configure -a
	./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) mawk
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for main in -lhts... no
checking for main in -lpthread... no
checking for main in -lz... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... no
checking for memmove... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
   dh_auto_build -a
	make -j4
make[1]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg'
make  all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg'
Making all in src
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/src'
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ivar.o ivar.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o alignment.o alignment.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o trim_primer_quality.o trim_primer_quality.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp
In file included from /usr/include/c++/9/vector:67,
                 from /usr/include/c++/9/regex:51,
                 from parse_gff.h:4,
                 from parse_gff.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/stl_vector.h:555:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  555 |    std::__uninitialized_copy_a(__x.begin(), __x.end(),
      |    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
  556 |           this->_M_impl._M_start,
      |           ~~~~~~~~~~~~~~~~~~~~~~~
  557 |           _M_get_Tp_allocator());
      |           ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:65,
                 from /usr/include/c++/9/regex:45,
                 from parse_gff.h:4,
                 from parse_gff.cpp:1:
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  305 |     __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  307 |     { return std::uninitialized_copy(__first, __last, __result); }
      |              ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
                 from /usr/include/c++/9/regex:51,
                 from parse_gff.h:4,
                 from parse_gff.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’} changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:65,
                 from /usr/include/c++/9/regex:45,
                 from parse_gff.h:4,
                 from parse_gff.cpp:1:
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*]’:
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  115 |     uninitialized_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  137 |       return std::__uninitialized_copy<__is_trivial(_ValueType1)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  138 |            && __is_trivial(_ValueType2)
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |            && __assignable>::
      |            ~~~~~~~~~~~~~~~~~~
  140 |  __uninit_copy(__first, __last, __result);
      |  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
                 from /usr/include/c++/9/regex:51,
                 from parse_gff.h:4,
                 from parse_gff.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’} changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:65,
                 from /usr/include/c++/9/regex:45,
                 from parse_gff.h:4,
                 from parse_gff.cpp:1:
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/stl_uninitialized.h:329:2: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  328 |       return std::__uninitialized_copy_a
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~
  329 |  (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  330 |   _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/usr/include/c++/9/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
   76 |         __uninit_copy(_InputIterator __first, _InputIterator __last,
      |         ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  305 |     __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  307 |     { return std::uninitialized_copy(__first, __last, __result); }
      |              ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*]’:
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  115 |     uninitialized_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  137 |       return std::__uninitialized_copy<__is_trivial(_ValueType1)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  138 |            && __is_trivial(_ValueType2)
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |            && __assignable>::
      |            ~~~~~~~~~~~~~~~~~~
  140 |  __uninit_copy(__first, __last, __result);
      |  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/usr/include/c++/9/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
   76 |         __uninit_copy(_InputIterator __first, _InputIterator __last,
      |         ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o -lhts -lz -lpthread -lhts -lz -lpthread
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/src'
Making all in tests
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg'
   dh_auto_test -a
	make -j4 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg'
Making check in src
make[2]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/src'
Making check in tests
make[2]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
make  check_primer_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_getmasked.o test_getmasked.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_removereads.o test_removereads.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_variants.o test_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_variants.o ../src/call_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_common_variants.o test_common_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp
In file included from /usr/include/c++/9/vector:67,
                 from /usr/include/c++/9/regex:51,
                 from ../src/parse_gff.h:4,
                 from ../src/parse_gff.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/stl_vector.h:555:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  555 |    std::__uninitialized_copy_a(__x.begin(), __x.end(),
      |    ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
  556 |           this->_M_impl._M_start,
      |           ~~~~~~~~~~~~~~~~~~~~~~~
  557 |           _M_get_Tp_allocator());
      |           ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
 1195 |    _M_realloc_insert(end(), __x);
      |    ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:65,
                 from /usr/include/c++/9/regex:45,
                 from ../src/parse_gff.h:4,
                 from ../src/parse_gff.cpp:1:
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  305 |     __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  307 |     { return std::uninitialized_copy(__first, __last, __result); }
      |              ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
                 from /usr/include/c++/9/regex:51,
                 from ../src/parse_gff.h:4,
                 from ../src/parse_gff.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  121 |    _M_realloc_insert(end(), std::forward<_Args>(__args)...);
      |    ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’} changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:65,
                 from /usr/include/c++/9/regex:45,
                 from ../src/parse_gff.h:4,
                 from ../src/parse_gff.cpp:1:
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*]’:
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  115 |     uninitialized_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
  137 |       return std::__uninitialized_copy<__is_trivial(_ValueType1)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  138 |            && __is_trivial(_ValueType2)
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |            && __assignable>::
      |            ~~~~~~~~~~~~~~~~~~
  140 |  __uninit_copy(__first, __last, __result);
      |  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
                 from /usr/include/c++/9/regex:51,
                 from ../src/parse_gff.h:4,
                 from ../src/parse_gff.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’} changed in GCC 7.1
  426 |       vector<_Tp, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/memory:65,
                 from /usr/include/c++/9/regex:45,
                 from ../src/parse_gff.h:4,
                 from ../src/parse_gff.cpp:1:
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator<gff3_feature>]’:
/usr/include/c++/9/bits/stl_uninitialized.h:329:2: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  328 |       return std::__uninitialized_copy_a
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~
  329 |  (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
      |  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  330 |   _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
      |   ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/usr/include/c++/9/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
   76 |         __uninit_copy(_InputIterator __first, _InputIterator __last,
      |         ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  305 |     __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  307 |     { return std::uninitialized_copy(__first, __last, __result); }
      |              ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*]’:
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  115 |     uninitialized_copy(_InputIterator __first, _InputIterator __last,
      |     ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
  137 |       return std::__uninitialized_copy<__is_trivial(_ValueType1)
      |              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  138 |            && __is_trivial(_ValueType2)
      |            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  139 |            && __assignable>::
      |            ~~~~~~~~~~~~~~~~~~
  140 |  __uninit_copy(__first, __last, __result);
      |  ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/usr/include/c++/9/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
   76 |         __uninit_copy(_InputIterator __first, _InputIterator __last,
      |         ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:76:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
g++ -DHAVE_CONFIG_H -I. -I..   -Wdate-time -D_FORTIFY_SOURCE=2  -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_common_variants test_common_variants.o ../src/get_common_variants.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_allele_depth test_allele_depth.o ../src/allele_functions.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_primer_bed test_primer_bed.o ../src/primer_bed.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o  -lhts -lz -lpthread
g++  -g -std=c++11 -Wall -Wextra -Werror  -Wl,-z,relro -Wl,-z,now -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o  -lhts -lz -lpthread
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
make  check-TESTS
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
make[4]: Entering directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
PASS: check_consensus
PASS: check_allele_depth
PASS: check_quality_trim
PASS: check_consensus_threshold
PASS: check_primer_bed
PASS: check_consensus_min_depth
PASS: check_getmasked
PASS: check_common_variants
FAIL: check_primer_trim
FAIL: check_unpaired_trim
PASS: check_variants
PASS: check_primer_trim_edge_cases
PASS: check_removereads
======================================
   ivar 1.2.2: tests/test-suite.log
======================================

# TOTAL: 13
# PASS:  11
# SKIP:  0
# XFAIL: 0
# FAIL:  2
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: check_primer_trim
=======================

Found 8 primers in BED file
[E::idx_find_and_load] Could not retrieve index file for '../data/test.unmapped.sorted.bam'
test_outside_primer
 ---- 
test_20_381_1:0:0_6:0:0_1_150
0-6 6-1 0-5 1-1 0-139 

Condensing cigar ... 
4-12 0-139 
 ---- 
test_20_381_1_softclip:0:0_6:0:0_1_150
4-24 0-3 2-2 0-1 1-1 0-4 2-1 6-1 2-1 0-114 

Condensing cigar ... 
4-33 0-114 
 ---- 
test_67_308_2:0:0_2:0:0_0_100
 ---- 
test_67_308_2:0:0_2:0:0_0_100
 ---- 
test_200_349_0:0:0_6:0:0_2_25
 ---- 
test_200_349_0:0:0_6:0:0_2_25
 ---- 
test_20_381_1:0:0_6:0:0_1_150
0-121 6-1 2-4 0-4 2-1 0-1 6-1 0-1 2-1 0-11 4-6 

Condensing cigar ... 
0-121 4-23 
 ---- 
test_20_381_1_softclip:0:0_6:0:0_1_150
0-103 1-1 0-10 1-1 0-13 4-24 

Condensing cigar ... 
0-103 4-49 
 ---- 
test_outside_primer
0-41 2-3 0-57 6-1 0-10 6-1 0-39 
Incorrect start position
Cigar flag didn't match for 6 ! Expected 2 Got 0
Cigar length didn't match for test_outside_primer ! Expected 3 Got 57
Cigar flag didn't match for 6 ! Expected 0 Got 6
Cigar length didn't match for test_outside_primer ! Expected 57 Got 1
Cigar flag didn't match for 6 ! Expected 6 Got 0
Cigar length didn't match for test_outside_primer ! Expected 1 Got 10
Cigar flag didn't match for 6 ! Expected 0 Got 6
Cigar length didn't match for test_outside_primer ! Expected 10 Got 1
Cigar flag didn't match for 6 ! Expected 6 Got 0
Cigar length didn't match for test_outside_primer ! Expected 1 Got 39

Condensing cigar ... 
4-23 0-75 6-1 0-10 6-1 0-39 
Cigar length didn't match after condense! Expected 18 Got 75
Cigar flag didn't match! Expected  Got 6
Cigar length didn't match after condense! Expected 3 Got 1
Cigar length didn't match after condense! Expected 57 Got 10
Cigar length didn't match after condense! Expected 10 Got 39
 ---- 
FAIL check_primer_trim (exit status: 255)

FAIL: check_unpaired_trim
=========================

Found 8 primers in BED file
test_72_280_12:1:0_11:0:0_2

Forward

Reverse
Cigar flag didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 0
Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 1
Cigar flag didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 0 Got 4
Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 1 Got 3
Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 3 Got 2
Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 8

Condensing cigar ... 
Cigar length didn't match after condense! Expected 93 Got 94
Cigar flag didn't match! Expected  Got 4
Cigar length didn't match after condense! Expected 2 Got 13
test_92_337_8:0:0_10:0:0_21

Forward

Reverse
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 56
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 56 Got 1
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 6
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 3
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 3 Got 99
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 99 Got 2
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 2 Got 65

Condensing cigar ... 
Cigar length didn't match after condense! Expected 19 Got 75
Cigar length didn't match after condense! Expected 56 Got 6
Cigar length didn't match after condense! Expected 1 Got 3
Cigar length didn't match after condense! Expected 6 Got 99
Cigar length didn't match after condense! Expected 3 Got 2
Cigar length didn't match after condense! Expected 99 Got 65
test_147_337_11:1:0_11:1:0_11

Forward

Reverse

Condensing cigar ... 
test_149_298_7:0:0_11:0:0_d

Forward

Reverse

Condensing cigar ... 
test_184_379_11:1:0_8:1:0_26

Forward

Reverse
Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 6 Got 0
Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 2 Got 89
Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 0 Got 4
Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 89 Got 18

Condensing cigar ... 
Cigar length didn't match after condense! Expected 71 Got 160
Cigar flag didn't match! Expected  Got 4
Cigar length didn't match after condense! Expected 2 Got 18
FAIL check_unpaired_trim (exit status: 255)

============================================================================
Testsuite summary for ivar 1.2.2
============================================================================
# TOTAL: 13
# PASS:  11
# SKIP:  0
# XFAIL: 0
# FAIL:  2
# XPASS: 0
# ERROR: 0
============================================================================
See tests/test-suite.log
Please report to gkarthik@scripps.edu
============================================================================
make[4]: *** [Makefile:826: test-suite.log] Error 1
make[4]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
make[3]: *** [Makefile:934: check-TESTS] Error 2
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
make[2]: *** [Makefile:1092: check-am] Error 2
make[2]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg/tests'
make[1]: *** [Makefile:360: check-recursive] Error 1
make[1]: Leaving directory '/<<BUILDDIR>>/ivar-1.2.2+dfsg'
dh_auto_test: error: make -j4 check VERBOSE=1 returned exit code 2
make: *** [debian/rules:9: binary-arch] Error 25
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2020-06-05T02:16:32Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 22144
Build-Time: 47
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 142
Job: ivar_1.2.2+dfsg-2
Machine Architecture: armhf
Package: ivar
Package-Time: 206
Source-Version: 1.2.2+dfsg-2
Space: 22144
Status: attempted
Version: 1.2.2+dfsg-2
--------------------------------------------------------------------------------
Finished at 2020-06-05T02:16:32Z
Build needed 00:03:26, 22144k disk space