idba →
1.1.3-3 →
armhf → 2018-09-27 04:57:09
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| idba 1.1.3-3 (armhf) Thu, 27 Sep 2018 04:50:34 +0000 |
+==============================================================================+
Package: idba
Version: 1.1.3-3
Source Version: 1.1.3-3
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-409c0033-5615-47d9-aa5c-c70d455a6e53' 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 [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 MB]
Fetched 23.9 MB in 11s (2195 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: 'idba' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/idba.git
Please use:
git clone https://salsa.debian.org/med-team/idba.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 454 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main idba 1.1.3-3 (dsc) [1889 B]
Get:2 http://172.17.0.1/private buster-staging/main idba 1.1.3-3 (tar) [446 kB]
Get:3 http://172.17.0.1/private buster-staging/main idba 1.1.3-3 (diff) [5896 B]
Fetched 454 kB in 0s (2042 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/idba-0Mn0oz/idba-1.1.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/idba-0Mn0oz' 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-jCO5B5/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-jCO5B5/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-jCO5B5/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-jCO5B5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (10.7 kB/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 74 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15689 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~)
Filtered Build-Depends: debhelper (>= 11~)
dpkg-deb: building package 'sbuild-build-depends-idba-dummy' in '/<<BUILDDIR>>/resolver-jCO5B5/apt_archive/sbuild-build-depends-idba-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-idba-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-jCO5B5/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ Sources [486 B]
Get:5 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ Packages [569 B]
Fetched 2388 B in 0s (12.7 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install idba 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 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 libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs 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 libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libfreetype6 libglib2.0-0 libgraphite2-3
libharfbuzz0b libicu-le-hb0 libicu60 libmagic-mgc libmagic1 libpipeline1
libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf
sbuild-build-depends-idba-dummy
0 upgraded, 36 newly installed, 0 to remove and 74 not upgraded.
Need to get 18.7 MB/19.2 MB of archives.
After this operation, 67.1 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-jCO5B5/apt_archive ./ sbuild-build-depends-idba-dummy 0.invalid.0 [852 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 2.8.4-2 [1161 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-4 [547 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.042-1 [20.1 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.042-1 [12.1 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.8.8-2+rpi1 [860 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:34 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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Setting up libarchive-zip-perl (1.64-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libelf1:armhf (0.170-0.5) ...
Setting up groff-base (1.22.3-10) ...
Setting up libglib2.0-0:armhf (2.58.1-2) ...
No schema files found: removed existing output file.
Setting up gettext-base (0.19.8.1-7) ...
Setting up libpipeline1:armhf (1.5.0-1) ...
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 (1:5.34-2) ...
Setting up libmagic1:armhf (1:5.34-2) ...
Setting up libgraphite2-3:armhf (1.3.12-1) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
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 (0.19.8.1-7) ...
Setting up libfile-stripnondeterminism-perl (0.042-1) ...
Setting up libharfbuzz0b:armhf (1.8.8-2+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up automake (1:1.16.1-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-4) ...
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 (0.19.8.1-7) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.3.5) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-idba-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.1.0-12+rpi1 gcc-8_8.1.0-12+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.1.0-12+rpi1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.3.5 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.042-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 e2fsprogs-l10n_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.1.0-12+rpi1 gcc_4:8.1.0-1+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+b19 gcc-5-base_5.5.0-8 gcc-8_8.1.0-12+rpi1 gcc-8-base_8.1.0-12+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gnupg_2.2.9-1+rpi1 gnupg-agent_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.1.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.1.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-12+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 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_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.042-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.1.0-12+rpi1 libgcc1_1:8.1.0-12+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_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.1.0-12+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libharfbuzz0b_1.8.8-2+rpi1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-7 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_239-7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-10 libperl5.24_5.24.1-7 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 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_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 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sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-idba-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 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 Fri Sep 21 20:59:41 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 ./idba_1.1.3-3.dsc
dpkg-source: info: extracting idba in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking idba_1.1.3.orig.tar.gz
dpkg-source: info: unpacking idba_1.1.3-3.debian.tar.xz
dpkg-source: info: applying install_all_idba_flavours.patch
dpkg-source: info: applying use-atomic-for-mips.patch
dpkg-source: info: applying spelling.patch
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=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-409c0033-5615-47d9-aa5c-c70d455a6e53
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package idba
dpkg-buildpackage: info: source version 1.1.3-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build idba-1.1.3
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
configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.ac:8: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
bin/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
bin/Makefile.am:9: warning: source file '$(top_srcdir)/src/tools/fa2fq.cpp' is in a subdirectory,
bin/Makefile.am:9: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
bin/Makefile.am:19: warning: source file '$(top_srcdir)/src/tools/filter_blat.cpp' is in a subdirectory,
bin/Makefile.am:19: but option 'subdir-objects' is disabled
bin/Makefile.am:17: warning: source file '$(top_srcdir)/src/tools/filter_contigs.cpp' is in a subdirectory,
bin/Makefile.am:17: but option 'subdir-objects' is disabled
bin/Makefile.am:33: warning: source file '$(top_srcdir)/src/release/filterfa.cpp' is in a subdirectory,
bin/Makefile.am:33: but option 'subdir-objects' is disabled
bin/Makefile.am:25: warning: source file '$(top_srcdir)/src/release/fq2fa.cpp' is in a subdirectory,
bin/Makefile.am:25: but option 'subdir-objects' is disabled
bin/Makefile.am:34: warning: source file '$(top_srcdir)/src/release/idba.cpp' is in a subdirectory,
bin/Makefile.am:34: but option 'subdir-objects' is disabled
bin/Makefile.am:30: warning: source file '$(top_srcdir)/src/release/idba_hybrid.cpp' is in a subdirectory,
bin/Makefile.am:30: but option 'subdir-objects' is disabled
bin/Makefile.am:29: warning: source file '$(top_srcdir)/src/release/idba_tran.cpp' is in a subdirectory,
bin/Makefile.am:29: but option 'subdir-objects' is disabled
bin/Makefile.am:13: warning: source file '$(top_srcdir)/src/tools/idba_tran_test.cpp' is in a subdirectory,
bin/Makefile.am:13: but option 'subdir-objects' is disabled
bin/Makefile.am:27: warning: source file '$(top_srcdir)/src/release/idba_ud.cpp' is in a subdirectory,
bin/Makefile.am:27: but option 'subdir-objects' is disabled
bin/Makefile.am:31: warning: source file '$(top_srcdir)/src/release/parallel_blat.cpp' is in a subdirectory,
bin/Makefile.am:31: but option 'subdir-objects' is disabled
bin/Makefile.am:18: warning: source file '$(top_srcdir)/src/tools/parallel_rna_blat.cpp' is in a subdirectory,
bin/Makefile.am:18: but option 'subdir-objects' is disabled
bin/Makefile.am:12: warning: source file '$(top_srcdir)/src/tools/print_graph.cpp' is in a subdirectory,
bin/Makefile.am:12: but option 'subdir-objects' is disabled
bin/Makefile.am:28: warning: source file '$(top_srcdir)/src/release/raw_n50.cpp' is in a subdirectory,
bin/Makefile.am:28: but option 'subdir-objects' is disabled
bin/Makefile.am:14: warning: source file '$(top_srcdir)/src/tools/sample_reads.cpp' is in a subdirectory,
bin/Makefile.am:14: but option 'subdir-objects' is disabled
bin/Makefile.am:7: warning: source file '$(top_srcdir)/src/tools/scaffold.cpp' is in a subdirectory,
bin/Makefile.am:7: but option 'subdir-objects' is disabled
bin/Makefile.am:6: warning: source file '$(top_srcdir)/src/tools/shuffle_reads.cpp' is in a subdirectory,
bin/Makefile.am:6: but option 'subdir-objects' is disabled
bin/Makefile.am:36: warning: source file '$(top_srcdir)/src/release/sim_reads.cpp' is in a subdirectory,
bin/Makefile.am:36: but option 'subdir-objects' is disabled
bin/Makefile.am:32: warning: source file '$(top_srcdir)/src/release/sim_reads_tran.cpp' is in a subdirectory,
bin/Makefile.am:32: but option 'subdir-objects' is disabled
bin/Makefile.am:15: warning: source file '$(top_srcdir)/src/tools/sort_psl.cpp' is in a subdirectory,
bin/Makefile.am:15: but option 'subdir-objects' is disabled
bin/Makefile.am:16: warning: source file '$(top_srcdir)/src/tools/sort_reads.cpp' is in a subdirectory,
bin/Makefile.am:16: but option 'subdir-objects' is disabled
bin/Makefile.am:20: warning: source file '$(top_srcdir)/src/tools/split_fa.cpp' is in a subdirectory,
bin/Makefile.am:20: but option 'subdir-objects' is disabled
bin/Makefile.am:23: warning: source file '$(top_srcdir)/src/tools/split_fq.cpp' is in a subdirectory,
bin/Makefile.am:23: but option 'subdir-objects' is disabled
bin/Makefile.am:35: warning: source file '$(top_srcdir)/src/release/split_scaffold.cpp' is in a subdirectory,
bin/Makefile.am:35: but option 'subdir-objects' is disabled
bin/Makefile.am:21: warning: source file '$(top_srcdir)/src/tools/test.cpp' is in a subdirectory,
bin/Makefile.am:21: but option 'subdir-objects' is disabled
bin/Makefile.am:8: warning: source file '$(top_srcdir)/src/tools/validate_component.cpp' is in a subdirectory,
bin/Makefile.am:8: but option 'subdir-objects' is disabled
bin/Makefile.am:26: warning: source file '$(top_srcdir)/src/release/validate_contigs_blat.cpp' is in a subdirectory,
bin/Makefile.am:26: but option 'subdir-objects' is disabled
bin/Makefile.am:11: warning: source file '$(top_srcdir)/src/tools/validate_contigs_mummer.cpp' is in a subdirectory,
bin/Makefile.am:11: but option 'subdir-objects' is disabled
bin/Makefile.am:22: warning: source file '$(top_srcdir)/src/tools/validate_reads_blat.cpp' is in a subdirectory,
bin/Makefile.am:22: but option 'subdir-objects' is disabled
bin/Makefile.am:10: warning: source file '$(top_srcdir)/src/tools/validate_rna.cpp' is in a subdirectory,
bin/Makefile.am:10: but option 'subdir-objects' is disabled
lib/Makefile.am:3: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/basic/math.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/hash_aligner.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/options_description.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/log.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/utils.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/blat_record.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/short_sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_reader.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_writer.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_io.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/compact_sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph_branch_group.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/scaffold_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph_branch_group.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_info.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/local_assembler.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/assembly_utility.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
lib/Makefile.am:68: but option 'subdir-objects' is disabled
lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest-all.cc' is in a subdirectory,
lib/Makefile.am:68: but option 'subdir-objects' is disabled
test/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
test/Makefile.am:11: warning: source file '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' is in a subdirectory,
test/Makefile.am:11: but option 'subdir-objects' is disabled
test/Makefile.am:8: warning: source file '$(top_srcdir)/src/test/bit_edges_unittest.cpp' is in a subdirectory,
test/Makefile.am:8: but option 'subdir-objects' is disabled
test/Makefile.am:6: warning: source file '$(top_srcdir)/src/test/compact_sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:6: but option 'subdir-objects' is disabled
test/Makefile.am:17: warning: source file '$(top_srcdir)/src/test/hash_map_unittest.cpp' is in a subdirectory,
test/Makefile.am:17: but option 'subdir-objects' is disabled
test/Makefile.am:10: warning: source file '$(top_srcdir)/src/test/hash_set_unittest.cpp' is in a subdirectory,
test/Makefile.am:10: but option 'subdir-objects' is disabled
test/Makefile.am:7: warning: source file '$(top_srcdir)/src/test/hash_table_unittest.cpp' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
test/Makefile.am:13: warning: source file '$(top_srcdir)/src/test/histgram_unittest.cpp' is in a subdirectory,
test/Makefile.am:13: but option 'subdir-objects' is disabled
test/Makefile.am:9: warning: source file '$(top_srcdir)/src/test/kmer_unittest.cpp' is in a subdirectory,
test/Makefile.am:9: but option 'subdir-objects' is disabled
test/Makefile.am:14: warning: source file '$(top_srcdir)/src/test/managed_list_unittest.cpp' is in a subdirectory,
test/Makefile.am:14: but option 'subdir-objects' is disabled
test/Makefile.am:15: warning: source file '$(top_srcdir)/src/test/sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:15: but option 'subdir-objects' is disabled
test/Makefile.am:16: warning: source file '$(top_srcdir)/src/test/short_sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:16: but option 'subdir-objects' is disabled
test/Makefile.am:12: warning: source file '$(top_srcdir)/src/test/vertex_status_unittest.cpp' is in a subdirectory,
test/Makefile.am:12: but option 'subdir-objects' is disabled
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- LDFLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" LIBS=" -latomic"
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" "LIBS= -latomic"
configure: WARNING: unrecognized options: --disable-maintainer-mode
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 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 for ranlib... ranlib
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
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 stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for working memcmp... yes
checking for vprintf... yes
checking for _doprnt... no
checking for sqrt... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating lib/Makefile
config.status: creating test/Makefile
config.status: creating script/Makefile
config.status: creating config.h
config.status: executing depfiles commands
configure: WARNING: unrecognized options: --disable-maintainer-mode
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in lib
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o math.o `test -f '../src/basic/math.cpp' || echo './'`../src/basic/math.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_aligner.o `test -f '../src/misc/hash_aligner.cpp' || echo './'`../src/misc/hash_aligner.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o options_description.o `test -f '../src/misc/options_description.cpp' || echo './'`../src/misc/options_description.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp
../src/misc/log.cpp: In destructor 'LogProcess::~LogProcess()':
../src/misc/log.cpp:78:58: warning: throw will always call terminate() [-Wterminate]
throw runtime_error("cannot kill log process");
^
../src/misc/log.cpp:78:58: note: in C++11 destructors default to noexcept
../src/misc/log.cpp: In static member function 'static void* LogThread::LogThreadFunc(void*)':
../src/misc/log.cpp:122:14: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
write(log_thread.out_fd, line, len);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp
In file included from /usr/include/c++/8/algorithm:62,
from ../src/basic/math.cpp:3:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../src/basic/math.cpp:3:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../src/basic/math.cpp:3:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void GenerateNormalCDFTable(int, int, std::vector<double>&)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o blat_record.o `test -f '../src/misc/blat_record.cpp' || echo './'`../src/misc/blat_record.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o short_sequence.o `test -f '../src/sequence/short_sequence.cpp' || echo './'`../src/sequence/short_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp
../src/graph/contig_graph.cpp: In member function 'void ContigGraph::TopSort(std::deque<ContigGraphVertexAdaptor>&, std::deque<ContigGraphVertexAdaptor>&)':
../src/graph/contig_graph.cpp:1391:30: warning: variable 'end' set but not used [-Wunused-but-set-variable]
ContigGraphVertexAdaptor end = GetEndVertexAdaptor(component);
^~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp
../src/assembly/local_assembler.cpp: In static member function 'static void* LocalAssemblerWithReference::LocalAssembleThread(void*)':
../src/assembly/local_assembler.cpp:488:22: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
bool flag = false;
^~~~
../src/assembly/local_assembler.cpp:489:21: warning: variable 'aligned' set but not used [-Wunused-but-set-variable]
int aligned[2] = {0};
^~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest-all.o `test -f '../gtest_src/gtest/gtest-all.cc' || echo './'`../gtest_src/gtest/gtest-all.cc
rm -f libassembly.a
ar cru libassembly.a math.o hash_aligner.o options_description.o log.o utils.o blat_record.o short_sequence.o sequence_reader.o sequence_writer.o sequence_io.o sequence.o compact_sequence.o contig_graph_branch_group.o hash_graph.o scaffold_graph.o contig_graph.o hash_graph_branch_group.o contig_info.o local_assembler.o assembly_utility.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libassembly.a
rm -f libgtest.a
ar cru libgtest.a gtest_main.o gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib'
Making all in bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/bin'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba.o `test -f '../src/release/idba.cpp' || echo './'`../src/release/idba.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_ud.o `test -f '../src/release/idba_ud.cpp' || echo './'`../src/release/idba_ud.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran.o `test -f '../src/release/idba_tran.cpp' || echo './'`../src/release/idba_tran.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp
../src/release/idba_tran.cpp: In function 'void FindIsoforms(ContigGraphPath&, std::deque<ContigGraphPath>&, ContigGraph&, std::deque<ContigGraphPath>&)':
../src/release/idba_tran.cpp:241:33: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (flag && path.size() > option.min_transcript)
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/release/idba_tran.cpp: In function 'void Assemble(HashGraph&)':
../src/release/idba_tran.cpp:523:35: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
if (transcripts[i].size() >= option.min_transcript)
~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o shuffle_reads.o `test -f '../src/tools/shuffle_reads.cpp' || echo './'`../src/tools/shuffle_reads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_component.o `test -f '../src/tools/validate_component.cpp' || echo './'`../src/tools/validate_component.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp
../src/tools/validate_component.cpp: In function 'int main(int, char**)':
../src/tools/validate_component.cpp:141:13: warning: unused variable 'ref_id' [-Wunused-variable]
int ref_id = dict[record.ref_name];
^~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp
../src/tools/validate_rna.cpp: In function 'int main(int, char**)':
../src/tools/validate_rna.cpp:396:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(flist, "%s %lf", buf, &coverage[i]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp
../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)':
../src/tools/validate_contigs_mummer.cpp:218:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:219:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:220:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:221:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:222:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fgets(line, MaxLine, fcoord);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_reads.o `test -f '../src/tools/sort_reads.cpp' || echo './'`../src/tools/sort_reads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_contigs.o `test -f '../src/tools/filter_contigs.cpp' || echo './'`../src/tools/filter_contigs.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_rna_blat.o `test -f '../src/tools/parallel_rna_blat.cpp' || echo './'`../src/tools/parallel_rna_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp
../src/tools/parallel_rna_blat.cpp: In function 'void CreateFile(const string&)':
../src/tools/parallel_rna_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void RemoveFile(const string&)':
../src/tools/parallel_rna_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void Append(const string&, const string&)':
../src/tools/parallel_rna_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void RunBlat(const string&)':
../src/tools/parallel_rna_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
~~~~~~^~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.cpp
../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive
#include "graph/contig_graph.h";
^
../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive
#include "sequence/sequence.h";
^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp
In file included from /usr/include/c++/8/vector:69,
from ../src/tools/validate_reads_blat.cpp:16:
/usr/include/c++/8/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++/8/bits/vector.tcc:478:5: 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>::
^~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp
In file included from /usr/include/c++/8/vector:64,
from ../src/tools/validate_reads_blat.cpp:16:
/usr/include/c++/8/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/8/bits/stl_vector.h:847:4: 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);
^~~~~~~~~~~~~~
../src/release/validate_contigs_blat.cpp: In function 'int main(int, char**)':
../src/release/validate_contigs_blat.cpp:388:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(flist, "%s %lf", buf, &coverage[i]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_blat.o `test -f '../src/release/parallel_blat.cpp' || echo './'`../src/release/parallel_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_tran.cpp
../src/release/parallel_blat.cpp: In function 'void CreateFile(const string&)':
../src/release/parallel_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void RemoveFile(const string&)':
../src/release/parallel_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void Append(const string&, const string&)':
../src/release/parallel_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void RunBlat(const string&)':
../src/release/parallel_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
~~~~~~^~~~~~~~~~~~~
../src/release/sim_reads_tran.cpp: In function 'int main(int, char**)':
../src/release/sim_reads_tran.cpp:89:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)', declared with attribute warn_unused_result [-Wunused-result]
fscanf(flist, "%s %lf", buf, &weight[i]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_scaffold.o `test -f '../src/release/split_scaffold.cpp' || echo './'`../src/release/split_scaffold.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sim_reads.o `test -f '../src/release/sim_reads.cpp' || echo './'`../src/release/sim_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba idba.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_ud idba_ud.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran idba_tran.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_hybrid idba_hybrid.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o shuffle_reads shuffle_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scaffold scaffold.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_component validate_component.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fa2fq fa2fq.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_rna validate_rna.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o print_graph print_graph.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sample_reads sample_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_psl sort_psl.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_reads sort_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_contigs filter_contigs.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_blat filter_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fa split_fa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o test test.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fq2fa fq2fa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o raw_n50 raw_n50.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_blat parallel_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads_tran sim_reads_tran.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filterfa filterfa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_scaffold split_scaffold.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads sim_reads.o ../lib/libassembly.a -latomic
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making all in test
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making all in script
make[3]: Entering directory '/<<PKGBUILDDIR>>/script'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/script'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in lib
make[2]: Entering directory '/<<PKGBUILDDIR>>/lib'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/lib'
Making check in bin
make[2]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making check in test
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
make compact_sequence_unittest hash_table_unittest bit_edges_unittest kmer_unittest hash_set_unittest atomic_integer_unittest vertex_status_unittest histgram_unittest managed_list_unittest sequence_unittest short_sequence_unittest hash_map_unittest
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o compact_sequence_unittest.o `test -f '../src/test/compact_sequence_unittest.cpp' || echo './'`../src/test/compact_sequence_unittest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_table_unittest.o `test -f '../src/test/hash_table_unittest.cpp' || echo './'`../src/test/hash_table_unittest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bit_edges_unittest.o `test -f '../src/test/bit_edges_unittest.cpp' || echo './'`../src/test/bit_edges_unittest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o kmer_unittest.o `test -f '../src/test/kmer_unittest.cpp' || echo './'`../src/test/kmer_unittest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_set_unittest.o `test -f '../src/test/hash_set_unittest.cpp' || echo './'`../src/test/hash_set_unittest.cpp
In file included from /usr/include/c++/8/set:60,
from ../gtest_src/gtest/gtest.h:2850,
from ../src/test/hash_table_unittest.cpp:9:
/usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const Kmer&>, std::tuple<>}; _Key = Kmer; _Val = std::pair<const Kmer, int>; _KeyOfValue = std::_Select1st<std::pair<const Kmer, int> >; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../src/test/hash_table_unittest.cpp:14:
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual void HashTableTest_Iterator_Test::TestBody()':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual void HashTableTest_Find_Test::TestBody()':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atomic_integer_unittest.o `test -f '../src/test/atomic_integer_unittest.cpp' || echo './'`../src/test/atomic_integer_unittest.cpp
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual void HashTableTest::SetUp()':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual void HashTableTest_WriteAndRead_Test::TestBody()':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vertex_status_unittest.o `test -f '../src/test/vertex_status_unittest.cpp' || echo './'`../src/test/vertex_status_unittest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o histgram_unittest.o `test -f '../src/test/histgram_unittest.cpp' || echo './'`../src/test/histgram_unittest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o managed_list_unittest.o `test -f '../src/test/managed_list_unittest.cpp' || echo './'`../src/test/managed_list_unittest.cpp
In file included from ../src/test/histgram_unittest.cpp:9:
../gtest_src/gtest/gtest.h: In instantiation of 'testing::AssertionResult testing::internal::CmpHelperEQ(const char*, const char*, const T1&, const T2&) [with T1 = int; T2 = unsigned int]':
../gtest_src/gtest/gtest.h:18417:23: required from 'static testing::AssertionResult testing::internal::EqHelper<true>::Compare(const char*, const char*, const T1&, const T2&, typename testing::internal::EnableIf<(! testing::internal::is_pointer<T2>::value)>::type*) [with T1 = int; T2 = unsigned int; typename testing::internal::EnableIf<(! testing::internal::is_pointer<T2>::value)>::type = void]'
../src/test/histgram_unittest.cpp:70:5: required from here
../gtest_src/gtest/gtest.h:18341:16: warning: comparison of integer expressions of different signedness: 'const int' and 'const unsigned int' [-Wsign-compare]
if (expected == actual) {
~~~~~~~~~^~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_unittest.o `test -f '../src/test/sequence_unittest.cpp' || echo './'`../src/test/sequence_unittest.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o short_sequence_unittest.o `test -f '../src/test/short_sequence_unittest.cpp' || echo './'`../src/test/short_sequence_unittest.cpp
In file included from /usr/include/c++/8/vector:69,
from ../gtest_src/gtest/gtest.h:55,
from ../src/test/histgram_unittest.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/8/bits/vector.tcc:413:7: 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++/8/algorithm:62,
from ../src/basic/histgram.h:16,
from ../src/test/histgram_unittest.cpp:11:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from ../gtest_src/gtest/gtest.h:55,
from ../src/test/histgram_unittest.cpp:9:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void HistgramTest::SetUp()':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../src/basic/histgram.h:16,
from ../src/test/histgram_unittest.cpp:11:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../src/basic/histgram.h:16,
from ../src/test/histgram_unittest.cpp:11:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In member function 'virtual void HistgramTest_Median_Test::TestBody()':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_map_unittest.o `test -f '../src/test/hash_map_unittest.cpp' || echo './'`../src/test/hash_map_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o compact_sequence_unittest compact_sequence_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_table_unittest hash_table_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o bit_edges_unittest bit_edges_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o kmer_unittest kmer_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_set_unittest hash_set_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o atomic_integer_unittest atomic_integer_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vertex_status_unittest vertex_status_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o histgram_unittest histgram_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o managed_list_unittest managed_list_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o short_sequence_unittest short_sequence_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sequence_unittest sequence_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
In file included from /usr/include/c++/8/set:60,
from ../gtest_src/gtest/gtest.h:2850,
from ../src/test/hash_map_unittest.cpp:9:
/usr/include/c++/8/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const Kmer&>, std::tuple<>}; _Key = Kmer; _Val = std::pair<const Kmer, int>; _KeyOfValue = std::_Select1st<std::pair<const Kmer, int> >; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]':
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../src/test/hash_map_unittest.cpp:13:
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual void HashMapTest_Iterator_Test::TestBody()':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual void HashMapTest::SetUp()':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function 'virtual void HashMapTest_Find_Test::TestBody()':
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const Kmer, int> >'} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wall -O3 -fopenmp -pthread -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_map_unittest hash_map_unittest.o ../lib/libassembly.a ../lib/libgtest.a -latomic
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make check-TESTS
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
PASS: bit_edges_unittest
PASS: compact_sequence_unittest
PASS: kmer_unittest
PASS: atomic_integer_unittest
PASS: vertex_status_unittest
PASS: managed_list_unittest
PASS: histgram_unittest
PASS: sequence_unittest
PASS: short_sequence_unittest
PASS: hash_set_unittest
PASS: hash_map_unittest
PASS: hash_table_unittest
============================================================================
Testsuite summary for idba 1.1.3
============================================================================
# TOTAL: 12
# PASS: 12
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making check in script
make[2]: Entering directory '/<<PKGBUILDDIR>>/script'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/script'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
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_installdirs -a
dh_auto_install -a
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/idba AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in lib
make[2]: Entering directory '/<<PKGBUILDDIR>>/lib'
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/lib'
Making install in bin
make[2]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[3]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/idba/usr/bin'
/usr/bin/install -c idba idba_ud idba_tran idba_hybrid '/<<PKGBUILDDIR>>/debian/idba/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bin'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making install in test
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making install in script
make[2]: Entering directory '/<<PKGBUILDDIR>>/script'
make[3]: Entering directory '/<<PKGBUILDDIR>>/script'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/idba/usr/bin'
/usr/bin/install -c scan.py run-unittest.py validate_blat validate_blat_parallel '/<<PKGBUILDDIR>>/debian/idba/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/script'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/script'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
# for the moment the role of these scripts is totally unknown but they do not seem to be necessary
mv debian/idba/usr/bin/*.py debian/idba/usr/lib/idba/
mv debian/idba/usr/bin/validate_blat* debian/idba/usr/lib/idba/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_tran contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_ud contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_hybrid 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/idba/usr/bin/idba_tran debian/idba/usr/bin/idba debian/idba/usr/bin/idba_ud debian/idba/usr/bin/idba_hybrid were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package idba: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package idba: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'idba' in '../idba_1.1.3-3_armhf.deb'.
dpkg-deb: building package 'idba-dbgsym' in '../idba-dbgsym_1.1.3-3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../idba_1.1.3-3_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build idba-1.1.3
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-09-27T04:57:00Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
idba_1.1.3-3_armhf.changes:
---------------------------
Format: 1.8
Date: Fri, 21 Sep 2018 22:55:54 +0200
Source: idba
Binary: idba
Architecture: armhf
Version: 1.1.3-3
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
idba - iterative De Bruijn Graph short read assemblers
Changes:
idba (1.1.3-3) unstable; urgency=medium
.
[ Steffen Moeller ]
* debian/copyright: Prepared exclusion of autogenerated files
* debian/control: bumped policy to 4.1.0 (no changes required)
* debian/upstream/metadata: yamllint cleanliness
.
[ Andreas Tille ]
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Do not parse d/changelog
Checksums-Sha1:
088728d45fa72fcf0affde18893f2581a59352eb 14436716 idba-dbgsym_1.1.3-3_armhf.deb
96a653b985a0077e4277971559e2dbaec26251a5 4572 idba_1.1.3-3_armhf.buildinfo
c171ea1a9a861efad7a43f73ec7934bb1b39bd5e 311408 idba_1.1.3-3_armhf.deb
Checksums-Sha256:
0224e89df664a45da66786f6b61ddd872c7297f3db0fc14b912dbbf061b174c7 14436716 idba-dbgsym_1.1.3-3_armhf.deb
3b52ee84a1775c42e4fa55901e0da1db227b45847698b8a2ea4e6d41e2d308cc 4572 idba_1.1.3-3_armhf.buildinfo
ec4c14e99dfbdb9897ab765ee747428121ff8aa6b18b593980a37317902481f7 311408 idba_1.1.3-3_armhf.deb
Files:
f1bdcc5a15fa231e75358256e4e38986 14436716 debug optional idba-dbgsym_1.1.3-3_armhf.deb
823aecb2376045cfc0dc7ee5ce22fc0c 4572 science optional idba_1.1.3-3_armhf.buildinfo
fa84c19acc8394c283da5fd121a4d859 311408 science optional idba_1.1.3-3_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
idba-dbgsym_1.1.3-3_armhf.deb
-----------------------------
new Debian package, version 2.0.
size 14436716 bytes: control archive=704 bytes.
483 bytes, 12 lines control
424 bytes, 4 lines md5sums
Package: idba-dbgsym
Source: idba
Version: 1.1.3-3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 14610
Depends: idba (= 1.1.3-3)
Section: debug
Priority: optional
Description: debug symbols for idba
Build-Ids: 0be04a4380ea0dc3f34c7774600649a55f74a32d 71dd36ba4b04e2da75b63b9611909d36f56f116f afe2897049f2e8ae4057ac5719bbdf7799f5d1bc bc0e698ab51b402d568f7bffeb11152e66434f42
drwxr-xr-x root/root 0 2018-09-21 20:55 ./
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/debug/.build-id/0b/
-rw-r--r-- root/root 3404008 2018-09-21 20:55 ./usr/lib/debug/.build-id/0b/e04a4380ea0dc3f34c7774600649a55f74a32d.debug
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/debug/.build-id/71/
-rw-r--r-- root/root 3606504 2018-09-21 20:55 ./usr/lib/debug/.build-id/71/dd36ba4b04e2da75b63b9611909d36f56f116f.debug
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/debug/.build-id/af/
-rw-r--r-- root/root 3997656 2018-09-21 20:55 ./usr/lib/debug/.build-id/af/e2897049f2e8ae4057ac5719bbdf7799f5d1bc.debug
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/debug/.build-id/bc/
-rw-r--r-- root/root 3938188 2018-09-21 20:55 ./usr/lib/debug/.build-id/bc/0e698ab51b402d568f7bffeb11152e66434f42.debug
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/share/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-09-21 20:55 ./usr/share/doc/idba-dbgsym -> idba
idba_1.1.3-3_armhf.deb
----------------------
new Debian package, version 2.0.
size 311408 bytes: control archive=1424 bytes.
1360 bytes, 27 lines control
855 bytes, 14 lines md5sums
Package: idba
Version: 1.1.3-3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2115
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libstdc++6 (>= 5.2), python
Section: science
Priority: optional
Homepage: https://github.com/loneknightpy/idba
Description: iterative De Bruijn Graph short read assemblers
IDBA stands for iterative de Bruijn graph assembler. In computational
sequence biology, an assembler solves the puzzle coming from large
sequencing machines that feature many gigabytes of short reads from a
large genome.
.
This package provides several flavours of the IDBA assembler, as they all
share the same source tree but serve different purposes and evolved over time.
.
IDBA is the basic iterative de Bruijn graph assembler for
second-generation sequencing reads. IDBA-UD, an extension of IDBA,
is designed to utilize paired-end reads to assemble low-depth regions
and use progressive depth on contigs to reduce errors in high-depth
regions. It is a generic purpose assembler and especially good for
single-cell and metagenomic sequencing data. IDBA-Hybrid is another
update version of IDBA-UD, which can make use of a similar reference
genome to improve assembly result. IDBA-Tran is an iterative de Bruijn
graph assembler for RNA-Seq data.
drwxr-xr-x root/root 0 2018-09-21 20:55 ./
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/bin/
-rwxr-xr-x root/root 504432 2018-09-21 20:55 ./usr/bin/idba
-rwxr-xr-x root/root 569968 2018-09-21 20:55 ./usr/bin/idba_hybrid
-rwxr-xr-x root/root 501300 2018-09-21 20:55 ./usr/bin/idba_tran
-rwxr-xr-x root/root 561776 2018-09-21 20:55 ./usr/bin/idba_ud
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/lib/idba/
-rwxr-xr-x root/root 496 2018-09-21 20:55 ./usr/lib/idba/run-unittest.py
-rwxr-xr-x root/root 4118 2018-09-21 20:55 ./usr/lib/idba/scan.py
-rwxr-xr-x root/root 301 2018-09-21 20:55 ./usr/lib/idba/validate_blat
-rwxr-xr-x root/root 223 2018-09-21 20:55 ./usr/lib/idba/validate_blat_parallel
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/share/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/share/doc/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/share/doc/idba/
-rw-r--r-- root/root 1147 2018-09-21 20:55 ./usr/share/doc/idba/changelog.Debian.gz
-rw-r--r-- root/root 1011 2018-09-21 20:55 ./usr/share/doc/idba/copyright
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/share/man/
drwxr-xr-x root/root 0 2018-09-21 20:55 ./usr/share/man/man1/
-rw-r--r-- root/root 751 2018-09-21 20:55 ./usr/share/man/man1/idba.1.gz
-rw-r--r-- root/root 860 2018-09-21 20:55 ./usr/share/man/man1/idba_hybrid.1.gz
-rw-r--r-- root/root 780 2018-09-21 20:55 ./usr/share/man/man1/idba_tran.1.gz
-rw-r--r-- root/root 828 2018-09-21 20:55 ./usr/share/man/man1/idba_ud.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 264680
Build-Time: 199
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 170
Job: idba_1.1.3-3
Machine Architecture: armhf
Package: idba
Package-Time: 386
Source-Version: 1.1.3-3
Space: 264680
Status: successful
Version: 1.1.3-3
--------------------------------------------------------------------------------
Finished at 2018-09-27T04:57:00Z
Build needed 00:06:26, 264680k disk space