dawg →
1.2-2 →
armhf → 2018-07-21 05:08:55
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| dawg 1.2-2 (armhf) Sat, 21 Jul 2018 04:59:19 +0000 |
+==============================================================================+
Package: dawg
Version: 1.2-2
Source Version: 1.2-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-0a9b257a-1348-4340-ad9e-09550ce62ce8' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.9 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.7 MB]
Fetched 23.6 MB in 29s (808 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: 'dawg' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/dawg.git
Please use:
git clone https://salsa.debian.org/med-team/dawg.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 190 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main dawg 1.2-2 (dsc) [1923 B]
Get:2 http://172.17.0.1/private buster-staging/main dawg 1.2-2 (tar) [180 kB]
Get:3 http://172.17.0.1/private buster-staging/main dawg 1.2-2 (diff) [7484 B]
Fetched 190 kB in 0s (989 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/dawg-oXwrRP/dawg-1.2' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/dawg-oXwrRP' 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-5KnBgs/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-5KnBgs/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-5KnBgs/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-5KnBgs/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (3277 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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libexpat1
libnss-systemd libpam-systemd libsasl2-modules libssl1.1 openssl
systemd-sysv
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 50 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-5KnBgs/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 (20.8 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15772 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), cmake, bison, flex
Filtered Build-Depends: debhelper (>= 11~), cmake, bison, flex
dpkg-deb: building package 'sbuild-build-depends-dawg-dummy' in '/<<BUILDDIR>>/resolver-5KnBgs/apt_archive/sbuild-build-depends-dawg-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-dawg-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-5KnBgs/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ Sources [499 B]
Get:5 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ Packages [583 B]
Fetched 2415 B in 1s (3618 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install dawg 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:
ca-certificates dbus dbus-user-session e2fsprogs-l10n libnss-systemd
libpam-systemd libsasl2-modules openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bison bsdmainutils cmake
cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file flex
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libarchive13 libbison-dev libbsd0 libcroco3 libcurl4 libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libicu-le-hb0 libicu60 libjsoncpp1
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzo2-2 libmagic-mgc
libmagic1 libnghttp2-14 libpipeline1 libpsl5 librhash0 librtmp1 libsigsegv2
libssh2-1 libtimedate-perl libtool libuv1 libxml2 m4 man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc bison-doc wamerican | wordlist
whois vacation cmake-doc ninja-build dh-make flex-doc gettext-doc
libasprintf-dev libgettextpo-dev groff lrzip krb5-doc krb5-user libtool-doc
gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
libfl-dev curl | wget | lynx 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 bison bsdmainutils cmake
cmake-data debhelper dh-autoreconf dh-strip-nondeterminism dwz file flex
gettext gettext-base groff-base intltool-debian libarchive-zip-perl
libarchive13 libbison-dev libbsd0 libcroco3 libcurl4 libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libgssapi-krb5-2 libharfbuzz0b libicu-le-hb0 libicu60 libjsoncpp1
libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblzo2-2 libmagic-mgc
libmagic1 libnghttp2-14 libpipeline1 libpsl5 librhash0 librtmp1 libsigsegv2
libssh2-1 libtimedate-perl libtool libuv1 libxml2 m4 man-db po-debconf
sbuild-build-depends-dawg-dummy
0 upgraded, 56 newly installed, 0 to remove and 50 not upgraded.
Need to get 26.6 MB/28.0 MB of archives.
After this operation, 96.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-5KnBgs/apt_archive ./ sbuild-build-depends-dawg-dummy 0.invalid.0 [868 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf flex armhf 2.6.4-6.1 [427 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-3 [234 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-3 [106 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-3 [64.7 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libbison-dev armhf 2:3.0.4.dfsg-1+b1 [433 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf bison armhf 2:3.0.4.dfsg-1+b1 [743 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf cmake-data all 3.11.2-1 [1386 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf liblzo2-2 armhf 2.10-0.1 [48.4 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.2-2 [832 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libarchive13 armhf 3.2.2-4 [252 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.32.0-1 [71.7 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.2-1 [52.5 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2 [54.0 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libcurl4 armhf 7.60.0-2 [281 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf librhash0 armhf 1.3.6-2 [97.2 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libuv1 armhf 1.21.0-2 [90.7 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf cmake armhf 3.11.2-1+b1 [2498 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.3.5 [981 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking sbuild-build-depends-dawg-dummy (0.invalid.0) ...
Setting up libarchive-zip-perl (1.60-1) ...
Setting up libnghttp2-14:armhf (1.32.0-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libuv1:armhf (1.21.0-2) ...
Setting up libpsl5:armhf (0.20.2-1) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.56.1-2) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-6) ...
Setting up cmake-data (3.11.2-1) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libbsd0:armhf (0.9.1-1) ...
Setting up libfreetype6:armhf (2.8.1-2) ...
Setting up libmagic-mgc (1:5.33-3) ...
Setting up libmagic1:armhf (1:5.33-3) ...
Setting up libgraphite2-3:armhf (1.3.11-2) ...
Setting up librhash0:armhf (1.3.6-2) ...
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libbison-dev:armhf (2:3.0.4.dfsg-1+b1) ...
Setting up bison (2:3.0.4.dfsg-1+b1) ...
update-alternatives: using /usr/bin/bison.yacc to provide /usr/bin/yacc (yacc) in auto mode
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
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 autopoint (0.19.8.1-6) ...
Setting up liblzo2-2:armhf (2.10-0.1) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up libjsoncpp1:armhf (1.7.4-3) ...
Setting up flex (2.6.4-6.1) ...
Setting up libharfbuzz0b:armhf (1.8.2-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.33-3) ...
Setting up libkrb5support0:armhf (1.16-2) ...
Setting up automake (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2.1) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up libcurl4:armhf (7.60.0-2) ...
Setting up dh-autoreconf (19) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.042-1) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up gettext (0.19.8.1-6) ...
Setting up libarchive13:armhf (3.2.2-4) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up cmake (3.11.2-1+b1) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.3.5) ...
Setting up sbuild-build-depends-dawg-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.8.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-21+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-19 gcc-7_7.3.0-19 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 linux-libc-dev_4.16.12-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3 binutils_2.30-21+rpi1 binutils-arm-linux-gnueabihf_2.30-21+rpi1 binutils-common_2.30-21+rpi1 bison_2:3.0.4.dfsg-1+b1 bsdmainutils_11.1.2 bsdutils_1:2.32-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 cmake_3.11.2-1+b1 cmake-data_3.11.2-1 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.3.0-3+rpi1 cpp-7_7.3.0-19 dash_0.5.8-2.10 dbus_1.12.8-3 dbus-user-session_1.12.8-3 debconf_1.5.67 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.8-1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.2-1 e2fsprogs_1.44.2-1 e2fsprogs-l10n_1.44.2-1 fakeroot_1.22-2 fdisk_2.32-0.1 file_1:5.33-3 findutils_4.6.0+git+20171230-2 flex_2.6.4-6.1 g++_4:7.3.0-3+rpi1 g++-7_7.3.0-19 gcc_4:7.3.0-3+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b7 gcc-5-base_5.5.0-8 gcc-7_7.3.0-19 gcc-7-base_7.3.0-19 gcc-8-base_8.1.0-8+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.8-1 gnupg-agent_2.2.8-1 gnupg-l10n_2.2.8-1 gnupg-utils_2.2.8-1 gpg_2.2.8-1 gpg-agent_2.2.8-1 gpg-wks-client_2.2.8-1 gpg-wks-server_2.2.8-1 gpgconf_2.2.8-1 gpgsm_2.2.8-1 gpgv_2.2.8-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.12-4 libapt-pkg5.0_1.6.1 libarchive-zip-perl_1.60-1 libarchive13_3.2.2-4 libargon2-0_0~20161029-2 libasan4_7.3.0-19 libassuan0_2.5.1-2 libatomic1_8.1.0-8+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.30-21+rpi1 libbison-dev_2:3.0.4.dfsg-1+b1 libblkid1_2.32-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-8+rpi1 libcilkrts5_7.3.0-19 libcom-err2_1.44.2-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl4_7.60.0-2 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.8-3 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.2-1 libfakeroot_1.22-2 libfdisk1_2.32-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-7-dev_7.3.0-19 libgcc1_1:8.1.0-8+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8.1.0-8+rpi1 libgpg-error0_1.31-1 libgraphite2-3_1.3.11-2 libgssapi-krb5-2_1.16-2 libharfbuzz0b_1.8.2-2 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl19_0.19-1 libjson-c3_0.12.1-1.3 libjsoncpp1_1.7.4-3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 liblzo2-2_2.10-0.1 libmagic-mgc_1:5.33-3 libmagic1_1:5.33-3 libmount1_2.32-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180210-4 libncurses6_6.1+20180210-4 libncursesw5_6.1+20180210-4 libncursesw6_6.1+20180210-4 libnettle6_3.4-1 libnghttp2-14_1.32.0-1 libnpth0_1.5-4 libnss-systemd_238-4 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.24_5.24.1-4 libperl5.26_5.26.2-6 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-1 libprocps7_2:3.3.15-2 libpsl5_0.20.2-1 libreadline7_7.0-5 librhash0_1.3.6-2 librtmp1_2.4+20151223.gitfa8646d.1-2 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-2 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.2-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0h-4 libstdc++-7-dev_7.3.0-19 libstdc++6_8.1.0-8+rpi1 libsystemd0_238-4 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo5_6.1+20180210-4 libtinfo6_6.1+20180210-4 libtool_2.4.6-2.1 libubsan0_7.3.0-19 libudev1_238-4 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.32-0.1 libuv1_1.21.0-2 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.12-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mount_2.32-0.1 multiarch-support_2.27-3+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180210-4 ncurses-bin_6.1+20180210-4 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-6 perl-base_5.26.2-6 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-6 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-dawg-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_238-4 util-linux_2.32-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jul 16 07:15:57 2018 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 ./dawg_1.2-2.dsc
dpkg-source: info: extracting dawg in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking dawg_1.2.orig.tar.gz
dpkg-source: info: unpacking dawg_1.2-2.debian.tar.xz
dpkg-source: info: applying 0001-Add-missing-include-of-cstring.patch
dpkg-source: info: applying 0003-Don-t-override-install-directories.patch
dpkg-source: info: applying 0004-Fix-typo-in-help-text.patch
dpkg-source: info: applying 0005-Remove-Encoding-add-Keywords-to-dawg.desktop.patch
dpkg-source: info: applying 0006-relative-path-in-test-script.patch
Check disc 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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-0a9b257a-1348-4340-ad9e-09550ce62ce8
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package dawg
dpkg-buildpackage: info: source version 1.2-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build dawg-1.2
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- \
-DCMAKE_LIBRARY_PATH=arm-linux-gnueabihf \
-DCMAKE_DATA_DIR=/usr/share/doc/dawg
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_LIBRARY_PATH=arm-linux-gnueabihf -DCMAKE_DATA_DIR=/usr/share/doc/dawg ..
-- The C compiler identification is GNU 7.3.0
-- The CXX compiler identification is GNU 7.3.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for bison
-- Looking for bison -- /usr/bin/bison
-- Looking for flex
-- Looking for flex -- /usr/bin/flex
-- Looking for unistd.h
-- Looking for unistd.h - found
-- Looking for process.h
-- Looking for process.h - not found
-- Looking for io.h
-- Looking for io.h - not found
-- Looking for getopt.h
-- Looking for getopt.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for getpid
-- Looking for getpid - found
-- Looking for _getpid
-- Looking for _getpid - not found
-- Looking for copysign
-- Looking for copysign - found
-- Looking for _copysign
-- Looking for _copysign - not found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for _snprintf
-- Looking for _snprintf - not found
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
CMAKE_LIBRARY_PATH
-- Build files have been written to: /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -H/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/dawg.dir/build.make src/CMakeFiles/dawg.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 7%] Generating parser.tab.cpp, parser.tab.hpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/bison --name-prefix=parser --defines --output-file=/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/parser.tab.cpp /<<PKGBUILDDIR>>/src/parser.ypp
[ 15%] Generating lex.parser.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/flex -Pparser -o/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/lex.parser.cpp /<<PKGBUILDDIR>>/src/parser.lpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/dawg.dir/DependInfo.cmake --color=
Scanning dependencies of target dawg
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/dawg.dir/build.make src/CMakeFiles/dawg.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[ 38%] Building CXX object src/CMakeFiles/dawg.dir/indel.cpp.o
[ 38%] Building CXX object src/CMakeFiles/dawg.dir/dawg.cpp.o
[ 38%] Building CXX object src/CMakeFiles/dawg.dir/eigen.cpp.o
[ 46%] Building CXX object src/CMakeFiles/dawg.dir/matrix.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -o CMakeFiles/dawg.dir/dawg.cpp.o -c /<<PKGBUILDDIR>>/src/dawg.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -o CMakeFiles/dawg.dir/indel.cpp.o -c /<<PKGBUILDDIR>>/src/indel.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -o CMakeFiles/dawg.dir/eigen.cpp.o -c /<<PKGBUILDDIR>>/src/eigen.cpp
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -o CMakeFiles/dawg.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/matrix.cpp
In file included from /<<PKGBUILDDIR>>/src/dawg.cpp:20:0:
/<<PKGBUILDDIR>>/src/tree.h:17:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSib;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/dawg.cpp:19:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dawg.cpp:20:0:
/<<PKGBUILDDIR>>/src/tree.h:18:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSub;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/dawg.cpp:19:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dawg.cpp:20:0:
/<<PKGBUILDDIR>>/src/tree.h:199:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pInsertionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/dawg.cpp:19:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dawg.cpp:20:0:
/<<PKGBUILDDIR>>/src/tree.h:200:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pDeletionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/dawg.cpp:19:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from /<<PKGBUILDDIR>>/src/dawg.h:42,
from /<<PKGBUILDDIR>>/src/indel.cpp:3:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /<<PKGBUILDDIR>>/src/dawg.h:42,
from /<<PKGBUILDDIR>>/src/indel.cpp:3:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'UserModel::UserModel(const std::vector<double>&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 53%] Building CXX object src/CMakeFiles/dawg.dir/output.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -o CMakeFiles/dawg.dir/output.cpp.o -c /<<PKGBUILDDIR>>/src/output.cpp
[ 61%] Building CXX object src/CMakeFiles/dawg.dir/rand.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -o CMakeFiles/dawg.dir/rand.cpp.o -c /<<PKGBUILDDIR>>/src/rand.cpp
[ 69%] Building CXX object src/CMakeFiles/dawg.dir/tree.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -o CMakeFiles/dawg.dir/tree.cpp.o -c /<<PKGBUILDDIR>>/src/tree.cpp
[ 76%] Building CXX object src/CMakeFiles/dawg.dir/var.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -o CMakeFiles/dawg.dir/var.cpp.o -c /<<PKGBUILDDIR>>/src/var.cpp
In file included from /usr/include/c++/7/vector:69:0,
from /<<PKGBUILDDIR>>/src/dawg.h:42,
from /<<PKGBUILDDIR>>/src/dawg.cpp:19:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/output.cpp:4:
/<<PKGBUILDDIR>>/src/tree.h:17:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSib;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/output.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/output.cpp:4:
/<<PKGBUILDDIR>>/src/tree.h:18:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSub;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/output.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/tree.cpp:4:0:
/<<PKGBUILDDIR>>/src/tree.h:17:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSib;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/tree.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/tree.cpp:4:0:
/<<PKGBUILDDIR>>/src/tree.h:18:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSub;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/tree.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/output.cpp:4:
/<<PKGBUILDDIR>>/src/tree.h:199:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pInsertionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/output.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/output.cpp:4:
/<<PKGBUILDDIR>>/src/tree.h:200:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pDeletionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/output.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/tree.cpp:4:0:
/<<PKGBUILDDIR>>/src/tree.h:199:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pInsertionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/tree.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/tree.cpp:4:0:
/<<PKGBUILDDIR>>/src/tree.h:200:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pDeletionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/tree.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/var.cpp:4:
/<<PKGBUILDDIR>>/src/tree.h:17:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSib;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/var.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/var.cpp:4:
/<<PKGBUILDDIR>>/src/tree.h:18:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSub;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/var.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/var.cpp:4:
/<<PKGBUILDDIR>>/src/tree.h:199:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pInsertionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/var.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/var.cpp:4:
/<<PKGBUILDDIR>>/src/tree.h:200:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pDeletionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/var.cpp:3:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from /<<PKGBUILDDIR>>/src/dawg.h:42,
from /<<PKGBUILDDIR>>/src/dawg.cpp:19:
/usr/include/c++/7/bits/stl_vector.h: In function 'bool Execute()':
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:712:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 84%] Building CXX object src/CMakeFiles/dawg.dir/lex.parser.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -I "/<<PKGBUILDDIR>>/src" -o CMakeFiles/dawg.dir/lex.parser.cpp.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/lex.parser.cpp
[ 92%] Building CXX object src/CMakeFiles/dawg.dir/parser.tab.cpp.o
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/c++ -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 "-DPACKAGE_STRING=\"dawg 1.2-release\"" "-DPACKAGE_BUGREPORT=\"reed@scit.us\"" -I "/<<PKGBUILDDIR>>/src" -o CMakeFiles/dawg.dir/parser.tab.cpp.o -c /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/parser.tab.cpp
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/parser.lpp:5:
/<<PKGBUILDDIR>>/src/tree.h:17:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSib;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/parser.lpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/parser.lpp:5:
/<<PKGBUILDDIR>>/src/tree.h:18:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSub;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/parser.lpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/parser.lpp:5:
/<<PKGBUILDDIR>>/src/tree.h:199:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pInsertionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/parser.lpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/parser.lpp:5:
/<<PKGBUILDDIR>>/src/tree.h:200:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pDeletionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/parser.lpp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/parser.ypp:5:
/<<PKGBUILDDIR>>/src/tree.h:17:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSib;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/parser.ypp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/parser.ypp:5:
/<<PKGBUILDDIR>>/src/tree.h:18:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<NewickNode> m_pSub;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/parser.ypp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/parser.ypp:5:
/<<PKGBUILDDIR>>/src/tree.h:199:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pInsertionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/parser.ypp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/var.h:7:0,
from /<<PKGBUILDDIR>>/src/parser.ypp:5:
/<<PKGBUILDDIR>>/src/tree.h:200:7: warning: 'template<class> class std::auto_ptr' is deprecated [-Wdeprecated-declarations]
std::auto_ptr<IndelModel> m_pDeletionModel;
^~~~~~~~
In file included from /usr/include/c++/7/bits/locale_conv.h:41:0,
from /usr/include/c++/7/locale:43,
from /usr/include/c++/7/iomanip:43,
from /<<PKGBUILDDIR>>/src/dawg.h:47,
from /<<PKGBUILDDIR>>/src/parser.ypp:4:
/usr/include/c++/7/bits/unique_ptr.h:51:28: note: declared here
template<typename> class auto_ptr;
^~~~~~~~
[100%] Linking CXX executable dawg
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/dawg.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dawg.dir/dawg.cpp.o CMakeFiles/dawg.dir/eigen.cpp.o CMakeFiles/dawg.dir/indel.cpp.o CMakeFiles/dawg.dir/matrix.cpp.o CMakeFiles/dawg.dir/output.cpp.o CMakeFiles/dawg.dir/rand.cpp.o CMakeFiles/dawg.dir/tree.cpp.o CMakeFiles/dawg.dir/var.cpp.o CMakeFiles/dawg.dir/lex.parser.cpp.o CMakeFiles/dawg.dir/parser.tab.cpp.o -o dawg
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target dawg
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# FIXME: This test fails - but let the build pass anyway for the moment
cd tests && PATH=$PATH:/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src sh test0.sh || true
2,3c2,3
< TCCTTGACCAGTTAGCAAGACGATATGCATCAAGTGCACTGGC---GTAAGTCTTTTTAC
< GCTGATCATA--TAGTCCGTATAGTCACTGAACGCCGTCCTCTCG
---
> AGGAACTGGTCACGTTCTGCTATACGTAGTTCACGTGACCGCATTCAGAAAAATGCGACT
> AGTATTGTGATCAGGCATATCAGTGACTTGCGGCAGGAGAGC
6,7c6,7
< TCGTTGGACAGT--GCAAGACGCTATGCATCAAGTGCACTGGCTAGGTAAGTGCGTTTAT
< GATGAGCACAACAGGTCCGGATAGTCCCTGAACGCTATACTCCCG
---
> AGCAACTTGTCACGTTCTGCGATACGTAGTTCACGTGACCGCATTCACGCAAACACTACT
> TGTGCT--GACCATGCATATCAGGGACTTGCGACATGTGGGC
10,11c10,11
< TCGA-CCCCAAA--TTAATACGTTAGTCATCAAGTGCACTGAC---GTAATAGCGTTTAT
< GATGATGAGTACTAGCCCGTGGAAACCCTAAAAGCGTTACCCCCG
---
> AGCATGGTGTCAAGTTCTGCGTTCAGTAGTTAACCAGACGGCATTAACGCTAATACATC-
> -GTGTT--GACCTACCAACGTACGGACTTGCGTAATGTGGTC
14,15c14,15
< TCGTTGAACAGT--GCAAGACGCTATGCATCAAGTGCACTGGC---GTAAGTGCGTTTAT
< GATGAACACAACTGGTCCGTATAGTCCCTGAACGCTGTACTCCCG
---
> AGCAACTTGTCACGTTCTGCGATACGTAGTTCACGTGACCGCATTCACGCAAATACTACT
> TGTGTT--GACCAGGCATATCAGGGACTTGCGACATGAGGGC
18,19c18,19
< TCGTACCACAGT--TCAAGACGCTAGGCATCAAGTGCACTGGC---GTAATTGCGTTTAT
< GATGGACACAACTAGTCCGTTGAATCCCTGAACGCTTTACCCCCG
---
> AGCATGGTGTCAAGTTCTGCGATCCGTAGTTCACGTGACCGCATTAACGCAAATACTACC
> TGTGTT--GATCAGGCAACTTAGGGACTTGCGAAATGGGGGC
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/dawg AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -H/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/dawg.dir/build.make src/CMakeFiles/dawg.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
cd /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/src/CMakeFiles/dawg.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make -f src/CMakeFiles/dawg.dir/build.make src/CMakeFiles/dawg.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[3]: Nothing to be done for 'src/CMakeFiles/dawg.dir/build'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
[100%] Built target dawg
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf/CMakeFiles 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<PKGBUILDDIR>>/debian/dawg/usr/bin/dawg
-- Installing: /<<PKGBUILDDIR>>/debian/dawg/usr/share/applications/dawg.desktop
-- Installing: /<<PKGBUILDDIR>>/debian/dawg/usr/share/pixmaps/dawg.png
-- Installing: /<<PKGBUILDDIR>>/debian/dawg/usr/share/doc/dawg/examples/example0.dawg
-- Installing: /<<PKGBUILDDIR>>/debian/dawg/usr/share/doc/dawg/examples/example1.dawg
-- Installing: /<<PKGBUILDDIR>>/debian/dawg/usr/share/doc/dawg/examples/example2.dawg
-- Installing: /<<PKGBUILDDIR>>/debian/dawg/usr/share/doc/dawg/examples/example3.dawg
-- Installing: /<<PKGBUILDDIR>>/debian/dawg/usr/share/doc/dawg/examples/example4.dawg
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-arm-linux-gnueabihf'
dh_install -a
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
chmod -x debian/dawg/usr/share/doc/dawg/examples/*
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/dawg/usr/bin/dawg contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/dawg/usr/bin/dawg was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'dawg' in '../dawg_1.2-2_armhf.deb'.
dpkg-deb: building package 'dawg-dbgsym' in '../dawg-dbgsym_1.2-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../dawg_1.2-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build dawg-1.2
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-07-21T05:08:45Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
dawg_1.2-2_armhf.changes:
-------------------------
Format: 1.8
Date: Mon, 16 Jul 2018 09:10:34 +0200
Source: dawg
Binary: dawg
Architecture: armhf
Version: 1.2-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
dawg - simulate the evolution of recombinant DNA sequences
Changes:
dawg (1.2-2) unstable; urgency=medium
.
[ Andreas Tille ]
* Team upload
* Add citation
* Homepage vanished but project is on Github - use this as homepage
* cme fix dpkg-control
* debhelper 11
* d/watch: version=4
* Fix short description
* run build time test and add autopkgtest
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.5
* Cleanup d/rules
.
[ Steffen Möller ]
* debian/upstream/metadata: Ref to OMICtools (Steffen Moeller)
Checksums-Sha1:
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49d6ff28a7ec98b271444887735457c62e38ab2c 5589 dawg_1.2-2_armhf.buildinfo
4ce037d9c97579988c47f2daac542b0d5f06f483 67676 dawg_1.2-2_armhf.deb
Checksums-Sha256:
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Files:
658b06f71659399eeabcd0dd80f01c95 595312 debug optional dawg-dbgsym_1.2-2_armhf.deb
45b5e0cdeeeae5a82c1db5dcf1a98c4f 5589 science optional dawg_1.2-2_armhf.buildinfo
4b48caca85addaa9f3befb354a7a3932 67676 science optional dawg_1.2-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
dawg-dbgsym_1.2-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 595312 bytes: control archive=528 bytes.
354 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: dawg-dbgsym
Source: dawg
Version: 1.2-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 621
Depends: dawg (= 1.2-2)
Section: debug
Priority: optional
Description: debug symbols for dawg
Build-Ids: a9f7ff0efa18c96329524072da01eb37bf663dc0
drwxr-xr-x root/root 0 2018-07-16 07:10 ./
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/lib/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/lib/debug/.build-id/a9/
-rw-r--r-- root/root 625276 2018-07-16 07:10 ./usr/lib/debug/.build-id/a9/f7ff0efa18c96329524072da01eb37bf663dc0.debug
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-07-16 07:10 ./usr/share/doc/dawg-dbgsym -> dawg
dawg_1.2-2_armhf.deb
--------------------
new Debian package, version 2.0.
size 67676 bytes: control archive=1456 bytes.
1015 bytes, 19 lines control
1422 bytes, 21 lines md5sums
Package: dawg
Version: 1.2-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 185
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: https://github.com/reedacartwright/dawg
Description: simulate the evolution of recombinant DNA sequences
DNA Assembly with Gaps (Dawg) is an application designed to simulate the
evolution of recombinant DNA sequences in continuous time based on the robust
general time reversible model with gamma and invariant rate heterogeneity and
a novel length-dependent model of gap formation. The application accepts
phylogenies in Newick format and can return the sequence of any node,
allowing for the exact evolutionary history to be recorded at the discretion
of users. Dawg records the gap history of every lineage to produce the true
alignment in the output. Many options are available to allow users to
customize their simulations and results.
drwxr-xr-x root/root 0 2018-07-16 07:10 ./
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/bin/
-rwxr-xr-x root/root 140472 2018-07-16 07:10 ./usr/bin/dawg
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/applications/
-rw-r--r-- root/root 292 2018-07-16 07:10 ./usr/share/applications/dawg.desktop
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/doc/dawg/
-rw-r--r-- root/root 206 2018-07-16 07:10 ./usr/share/doc/dawg/README.Debian
-rw-r--r-- root/root 348 2018-07-16 07:10 ./usr/share/doc/dawg/README.test
-rw-r--r-- root/root 468 2018-07-16 07:10 ./usr/share/doc/dawg/changelog.Debian.gz
-rw-r--r-- root/root 827 2009-04-26 05:14 ./usr/share/doc/dawg/changelog.gz
-rw-r--r-- root/root 5496 2018-07-16 07:10 ./usr/share/doc/dawg/copyright
-rw-r--r-- root/root 3062 2018-07-16 07:10 ./usr/share/doc/dawg/dawg.txt
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/doc/dawg/examples/
-rw-r--r-- root/root 219 2009-04-26 05:14 ./usr/share/doc/dawg/examples/example0.dawg
-rw-r--r-- root/root 629 2009-04-26 05:14 ./usr/share/doc/dawg/examples/example1.dawg
-rw-r--r-- root/root 336 2009-04-26 05:14 ./usr/share/doc/dawg/examples/example2.dawg
-rw-r--r-- root/root 443 2009-04-26 05:14 ./usr/share/doc/dawg/examples/example3.dawg
-rw-r--r-- root/root 338 2009-04-26 05:14 ./usr/share/doc/dawg/examples/example4.dawg
-rw-r--r-- root/root 255 2009-04-26 05:14 ./usr/share/doc/dawg/news.txt
-rw-r--r-- root/root 4583 2009-04-26 05:14 ./usr/share/doc/dawg/readme.txt.gz
-rw-r--r-- root/root 287 2018-07-16 07:10 ./usr/share/doc/dawg/run-unit-test
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/doc/dawg/tests/
-rw-r--r-- root/root 236 2009-04-26 05:14 ./usr/share/doc/dawg/tests/test0.dawg
-rw-r--r-- root/root 540 2009-04-26 05:14 ./usr/share/doc/dawg/tests/test0.fasta
-rw-r--r-- root/root 113 2018-07-16 07:10 ./usr/share/doc/dawg/tests/test0.sh
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/man/
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/man/man1/
-rw-r--r-- root/root 1910 2018-07-16 07:10 ./usr/share/man/man1/dawg.1.gz
drwxr-xr-x root/root 0 2018-07-16 07:10 ./usr/share/pixmaps/
-rw-r--r-- root/root 2564 2009-04-26 05:14 ./usr/share/pixmaps/dawg.png
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 8148
Build-Time: 141
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 372
Job: dawg_1.2-2
Machine Architecture: armhf
Package: dawg
Package-Time: 566
Source-Version: 1.2-2
Space: 8148
Status: successful
Version: 1.2-2
--------------------------------------------------------------------------------
Finished at 2018-07-21T05:08:45Z
Build needed 00:09:26, 8148k disc space