idba →
1.1.3-1 →
armhf → 2017-06-17 23:07:13
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| idba 1.1.3-1 (armhf) Sat, 17 Jun 2017 22:51:38 +0000 |
+==============================================================================+
Package: idba
Version: 1.1.3-1
Source Version: 1.1.3-1
Distribution: stretch-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/stretch-staging-armhf-sbuild-944a2d7a-f013-4bb6-b8f3-2ba389e18389' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private stretch-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private stretch-staging/main Sources [9733 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf Packages [11.7 MB]
Fetched 21.4 MB in 24s (868 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://anonscm.debian.org/git/debian-med/idba.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/idba.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 453 kB of source archives.
Get:1 http://172.17.0.1/private stretch-staging/main idba 1.1.3-1 (dsc) [1884 B]
Get:2 http://172.17.0.1/private stretch-staging/main idba 1.1.3-1 (tar) [446 kB]
Get:3 http://172.17.0.1/private stretch-staging/main idba 1.1.3-1 (diff) [4652 B]
Fetched 453 kB in 0s (6311 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/idba-XnFjO5/idba-1.1.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/idba-XnFjO5' 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-7dpF5P/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-7dpF5P/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-7dpF5P/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ Packages [429 B]
Fetched 2105 B in 0s (3244 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
fuse2fs gnupg-l10n libfuse2 manpages
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 0 not upgraded.
Need to get 770 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [770 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13974 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 (>= 9), dh-autoreconf
Filtered Build-Depends: debhelper (>= 9), dh-autoreconf
dpkg-deb: building package 'sbuild-build-depends-idba-dummy' in '/<<BUILDDIR>>/resolver-7dpF5P/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-7dpF5P/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ Sources [493 B]
Get:5 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ Packages [569 B]
Fetched 2395 B in 0s (3376 B/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:
fuse2fs gnupg-l10n libfuse2 manpages
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 file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtool libunistring0 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 less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx-cur libglib2.0-data shared-mime-info xdg-user-dirs
libltdl-dev xml-core libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libbsd0 libcroco3 libffi6
libfile-stripnondeterminism-perl libglib2.0-0 libicu57 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtool libunistring0 libxml2 m4 man-db
po-debconf sbuild-build-depends-idba-dummy
0 upgraded, 31 newly installed, 0 to remove and 0 not upgraded.
Need to get 19.1 MB/19.1 MB of archives.
After this operation, 64.8 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-7dpF5P/apt_archive ./ sbuild-build-depends-idba-dummy 0.invalid.0 [780 B]
Get:2 http://172.17.0.1/private stretch-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private stretch-staging/main armhf libbsd0 armhf 0.8.3-1 [89.0 kB]
Get:4 http://172.17.0.1/private stretch-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private stretch-staging/main armhf libpipeline1 armhf 1.4.1-2 [23.7 kB]
Get:6 http://172.17.0.1/private stretch-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private stretch-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:8 http://172.17.0.1/private stretch-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:9 http://172.17.0.1/private stretch-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:10 http://172.17.0.1/private stretch-staging/main armhf gettext-base armhf 0.19.8.1-2 [116 kB]
Get:11 http://172.17.0.1/private stretch-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:12 http://172.17.0.1/private stretch-staging/main armhf libxml2 armhf 2.9.4+dfsg1-2.2 [806 kB]
Get:13 http://172.17.0.1/private stretch-staging/main armhf libsigsegv2 armhf 2.10-5 [28.4 kB]
Get:14 http://172.17.0.1/private stretch-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:15 http://172.17.0.1/private stretch-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:16 http://172.17.0.1/private stretch-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:17 http://172.17.0.1/private stretch-staging/main armhf automake all 1:1.15-6 [733 kB]
Get:18 http://172.17.0.1/private stretch-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:19 http://172.17.0.1/private stretch-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:20 http://172.17.0.1/private stretch-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:21 http://172.17.0.1/private stretch-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:22 http://172.17.0.1/private stretch-staging/main armhf libfile-stripnondeterminism-perl all 0.034-1 [16.4 kB]
Get:23 http://172.17.0.1/private stretch-staging/main armhf dh-strip-nondeterminism all 0.034-1 [10.5 kB]
Get:24 http://172.17.0.1/private stretch-staging/main armhf libglib2.0-0 armhf 2.50.3-2 [2527 kB]
Get:25 http://172.17.0.1/private stretch-staging/main armhf libcroco3 armhf 0.6.11-3 [131 kB]
Get:26 http://172.17.0.1/private stretch-staging/main armhf libunistring0 armhf 0.9.6+really0.9.3-0.1 [252 kB]
Get:27 http://172.17.0.1/private stretch-staging/main armhf gettext armhf 0.19.8.1-2 [1434 kB]
Get:28 http://172.17.0.1/private stretch-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:29 http://172.17.0.1/private stretch-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:30 http://172.17.0.1/private stretch-staging/main armhf debhelper all 10.2.5 [961 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 13974 files and directories currently installed.)
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Setting up libarchive-zip-perl (1.59-1) ...
Setting up libsigsegv2:armhf (2.10-5) ...
Setting up groff-base (1.22.3-9) ...
Setting up gettext-base (0.19.8.1-2) ...
Setting up libpipeline1:armhf (1.4.1-2) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.3-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-2.2) ...
Setting up libmagic-mgc (1:5.30-1) ...
Setting up libmagic1:armhf (1:5.30-1) ...
Processing triggers for libc-bin (2.24-11) ...
Setting up autotools-dev (20161112.1) ...
Setting up libunistring0:armhf (0.9.6+really0.9.3-0.1) ...
Setting up libffi6:armhf (3.2.1-6) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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 (0.19.8.1-2) ...
Setting up libfile-stripnondeterminism-perl (0.034-1) ...
Setting up libglib2.0-0:armhf (2.50.3-2) ...
No schema files found: doing nothing.
Setting up autoconf (2.69-10) ...
Setting up file (1:5.30-1) ...
Setting up libcroco3:armhf (0.6.11-3) ...
Setting up automake (1:1.15-6) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-2) ...
Setting up gettext (0.19.8.1-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (14) ...
Setting up dh-strip-nondeterminism (0.034-1) ...
Setting up debhelper (10.2.5) ...
Setting up sbuild-build-depends-idba-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-11) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-5 dpkg-dev_1.18.24 g++-6_6.3.0-18+rpi1 gcc-6_6.3.0-18+rpi1 libc6-dev_2.24-11 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: acl_2.2.52-3 adduser_3.115 apt_1.4.6 autoconf_2.69-10 automake_1:1.15-6 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_9.9+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-5 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-1 build-essential_12.3 bzip2_1.0.6-8.1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4 cpp-6_6.3.0-18+rpi1 dash_0.5.8-2.4 debconf_1.5.61 debfoster_2.7-2.1 debhelper_10.2.5 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.034-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20161106-2 fuse2fs_1.43.4-2 g++_4:6.3.0-4 g++-6_6.3.0-18+rpi1 gcc_4:6.3.0-4 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_4.9.3-14 gcc-6_6.3.0-18+rpi1 gcc-6-base_6.3.0-18+rpi1 gettext_0.19.8.1-2 gettext-base_0.19.8.1-2 gnupg_2.1.18-6 gnupg-agent_2.1.18-6 gnupg-l10n_2.1.18-6 gpgv_2.1.18-6 grep_2.27-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 init_1.48 init-system-helpers_1.48 initscripts_2.88dsf-59.9 insserv_1.14.0-5.4 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_23-2 libacl1_2.2.52-3 libapparmor1_2.11.0-3 libapt-pkg4.12_1.0.9.10 libapt-pkg5.0_1.4.6 libarchive-zip-perl_1.59-1 libasan1_4.9.3-14 libasan3_6.3.0-18+rpi1 libassuan0_2.4.3-2 libatomic1_6.3.0-18+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.6.7-2 libaudit1_1:2.6.7-2 libblkid1_2.29.2-1 libbsd0_0.8.3-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-11 libc-dev-bin_2.24-11 libc6_2.24-11 libc6-dev_2.24-11 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcap2-bin_1:2.25-1 libcc1-0_6.3.0-18+rpi1 libcomerr2_1.43.4-2 libcroco3_0.6.11-3 libcryptsetup4_2:1.7.3-4 libdb5.3_5.3.28-12 libdbus-1-3_1.10.18-1 libdebconfclient0_0.227 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.74-1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.034-1 libfuse2_2.9.7-1 libgc1c2_1:7.4.2-8 libgcc-4.9-dev_4.9.3-14 libgcc-6-dev_6.3.0-18+rpi1 libgcc1_1:6.3.0-18+rpi1 libgcrypt20_1.7.6-2 libgdbm3_1.8.3-14 libglib2.0-0_2.50.3-2 libgmp10_2:6.1.2+dfsg-1 libgomp1_6.3.0-18+rpi1 libgpg-error0_1.26-2 libicu57_57.1-6 libidn11_1.33-1 libip4tc0_1.6.0+snapshot20161117-6 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_23-2 libksba8_1.3.5-2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.2 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmount1_2.29.2-1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20161126-1 libncursesw5_6.0+20161126-1 libnpth0_1.3-1 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-3 libpipeline1_1.4.1-2 libpng12-0_1.2.54-6 libprocps3_2:3.3.9-9 libprocps6_2:3.3.12-3 libreadline7_7.0-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.10-5 libslang2_2.3.1-5 libsmartcols1_2.29.2-1 libsqlite3-0_3.16.2-5 libss2_1.43.4-2 libstdc++-4.9-dev_4.9.3-14 libstdc++-6-dev_6.3.0-18+rpi1 libstdc++6_6.3.0-18+rpi1 libsystemd0_232-25 libtimedate-perl_2.3000-2 libtinfo5_6.0+20161126-1 libtool_2.4.6-2 libubsan0_6.3.0-18+rpi1 libudev1_232-25 libunistring0_0.9.6+really0.9.3-0.1 libusb-0.1-4_2:0.1.12-30 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-1 libxml2_2.9.4+dfsg1-2.2 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 manpages_4.10-2 mawk_1.3.3-17 mount_2.29.2-1 multiarch-support_2.24-11 nano_2.7.4-1 ncurses-base_6.0+20161126-1 ncurses-bin_6.0+20161126-1 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.24.1-3 perl-base_5.24.1-3 perl-modules-5.24_5.24.1-3 pinentry-curses_1.0.0-2 po-debconf_1.0.20 procps_2:3.3.12-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-idba-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9 startpar_0.59-3.1 systemd_232-25 systemd-sysv_232-25 sysv-rc_2.88dsf-59.9 sysvinit-utils_2.88dsf-59.9 tar_1.29b-1.1 tzdata_2017b-1 udev_232-25 util-linux_2.29.2-1 xz-utils_5.2.2-1.2 zlib1g_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| 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 Aug 5 22:18:35 2016 UTC
gpgv: using RSA key 578A0494D1C646D1
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./idba_1.1.3-1.dsc
dpkg-source: info: extracting idba in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking idba_1.1.3.orig.tar.gz
dpkg-source: info: unpacking idba_1.1.3-1.debian.tar.xz
dpkg-source: info: applying use-atomic-for-mips.patch
dpkg-source: info: applying spelling.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=stretch-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=stretch-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=stretch-staging-armhf-sbuild-944a2d7a-f013-4bb6-b8f3-2ba389e18389
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package idba
dpkg-buildpackage: info: source version 1.1.3-1
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 --with autoreconf --parallel
dh_testdir -O--parallel
dh_auto_clean -O--parallel
dh_autoreconf_clean -O--parallel
dh_clean -O--parallel
debian/rules build-arch
dh build-arch --with autoreconf --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
dh_autoreconf -a -O--parallel
configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.ac:8: http://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 --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 for style of include used by make... GNU
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 -O--parallel
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:122:44: 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++/6/algorithm:62:0,
from ../src/basic/math.cpp:3:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from ../src/basic/math.cpp:3:
/usr/include/c++/6/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++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from ../src/basic/math.cpp:3:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In function 'void GenerateNormalCDFTable(int, int, std::vector<double>&)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change 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
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
../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-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_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.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 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
../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 fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.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_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:396:55: 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
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
../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)':
../src/tools/validate_contigs_mummer.cpp:218:33: 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:219:33: 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:220:33: 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:221:33: 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:222:33: 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 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:47:24: 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:53:24: 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:59:24: 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:96:32: 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++/6/vector:69:0,
from ../src/tools/validate_reads_blat.cpp:16:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change 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++/6/vector:64:0,
from ../src/tools/validate_reads_blat.cpp:16:
/usr/include/c++/6/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/6/bits/stl_vector.h:1055:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
../src/release/validate_contigs_blat.cpp: In function 'int main(int, char**)':
../src/release/validate_contigs_blat.cpp:388:55: 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 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 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 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 parallel_blat.o `test -f '../src/release/parallel_blat.cpp' || echo './'`../src/release/parallel_blat.cpp
../src/release/parallel_blat.cpp: In function 'void CreateFile(const string&)':
../src/release/parallel_blat.cpp:47:24: 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:53:24: 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:59:24: 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:96:32: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(cmd.c_str());
^
../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 between signed and unsigned integer expressions [-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 between signed and unsigned integer expressions [-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 sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_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 filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp
../src/release/sim_reads_tran.cpp: In function 'int main(int, char**)':
../src/release/sim_reads_tran.cpp:89:49: 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 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 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_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 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 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
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 idba.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 -O--parallel
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++/6/set:60:0,
from ../gtest_src/gtest/gtest.h:2850,
from ../src/test/hash_table_unittest.cpp:9:
/usr/include/c++/6/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++/6/bits/stl_tree.h:2193:7: 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> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from ../src/test/hash_table_unittest.cpp:14:
/usr/include/c++/6/bits/stl_map.h: In member function 'virtual void HashTableTest_Iterator_Test::TestBody()':
/usr/include/c++/6/bits/stl_map.h:483:4: 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> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'virtual void HashTableTest_Find_Test::TestBody()':
/usr/include/c++/6/bits/stl_map.h:483:4: 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> >}' will change 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++/6/bits/stl_map.h: In member function 'virtual void HashTableTest::SetUp()':
/usr/include/c++/6/bits/stl_map.h:483:4: 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> >}' will change 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
/usr/include/c++/6/bits/stl_map.h: In member function 'virtual void HashTableTest_WriteAndRead_Test::TestBody()':
/usr/include/c++/6/bits/stl_map.h:483:4: 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> >}' will change 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 histgram_unittest.o `test -f '../src/test/histgram_unittest.cpp' || echo './'`../src/test/histgram_unittest.cpp
In file included from ../src/test/histgram_unittest.cpp:9:0:
../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 between signed and unsigned integer expressions [-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 managed_list_unittest.o `test -f '../src/test/managed_list_unittest.cpp' || echo './'`../src/test/managed_list_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 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++/6/algorithm:62:0,
from ../src/basic/histgram.h:16,
from ../src/test/histgram_unittest.cpp:11:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from ../src/basic/histgram.h:16,
from ../src/test/histgram_unittest.cpp:11:
/usr/include/c++/6/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++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from ../src/basic/histgram.h:16,
from ../src/test/histgram_unittest.cpp:11:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'virtual void HistgramTest_Median_Test::TestBody()':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change 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++/6/set:60:0,
from ../gtest_src/gtest/gtest.h:2850,
from ../src/test/hash_map_unittest.cpp:9:
/usr/include/c++/6/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++/6/bits/stl_tree.h:2193:7: 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> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:61:0,
from ../src/test/hash_map_unittest.cpp:13:
/usr/include/c++/6/bits/stl_map.h: In member function 'virtual void HashMapTest_Iterator_Test::TestBody()':
/usr/include/c++/6/bits/stl_map.h:483:4: 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> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'virtual void HashMapTest_Find_Test::TestBody()':
/usr/include/c++/6/bits/stl_map.h:483:4: 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> >}' will change in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/6/bits/stl_map.h: In member function 'virtual void HashMapTest::SetUp()':
/usr/include/c++/6/bits/stl_map.h:483:4: 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> >}' will change 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: kmer_unittest
PASS: compact_sequence_unittest
PASS: bit_edges_unittest
PASS: atomic_integer_unittest
PASS: vertex_status_unittest
PASS: histgram_unittest
PASS: managed_list_unittest
PASS: sequence_unittest
PASS: short_sequence_unittest
PASS: hash_set_unittest
FAIL: hash_table_unittest
PASS: hash_map_unittest
=====================================
idba 1.1.3: test/test-suite.log
=====================================
# TOTAL: 12
# PASS: 11
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
.. contents:: :depth: 2
FAIL: hash_table_unittest
=========================
Running main() from gtest_main.cc
[==========] Running 13 tests from 1 test case.
[----------] Global test environment set-up.
[----------] 13 tests from HashTableTest
[ RUN ] HashTableTest.DefaultConstructor
[ OK ] HashTableTest.DefaultConstructor (141 ms)
[ RUN ] HashTableTest.CopyConstructor
[ OK ] HashTableTest.CopyConstructor (163 ms)
[ RUN ] HashTableTest.Iterator
[ OK ] HashTableTest.Iterator (167 ms)
[ RUN ] HashTableTest.InsertUnique
[ OK ] HashTableTest.InsertUnique (161 ms)
[ RUN ] HashTableTest.Find
[ OK ] HashTableTest.Find (140 ms)
[ RUN ] HashTableTest.Remove
[ OK ] HashTableTest.Remove (126 ms)
[ RUN ] HashTableTest.RemoveIf
[ OK ] HashTableTest.RemoveIf (93 ms)
[ RUN ] HashTableTest.ForEach
../src/test/hash_table_unittest.cpp:180: Failure
Value of: counter.count
Actual: 9906
Expected: simple_hash_table.size()
Which is: 10000
[ FAILED ] HashTableTest.ForEach (94 ms)
[ RUN ] HashTableTest.Size
[ OK ] HashTableTest.Size (85 ms)
[ RUN ] HashTableTest.Empty
[ OK ] HashTableTest.Empty (85 ms)
[ RUN ] HashTableTest.Swap
[ OK ] HashTableTest.Swap (106 ms)
[ RUN ] HashTableTest.Clear
[ OK ] HashTableTest.Clear (100 ms)
[ RUN ] HashTableTest.WriteAndRead
[ OK ] HashTableTest.WriteAndRead (211 ms)
[----------] 13 tests from HashTableTest (1689 ms total)
[----------] Global test environment tear-down
[==========] 13 tests from 1 test case ran. (1691 ms total)
[ PASSED ] 12 tests.
[ FAILED ] 1 test, listed below:
[ FAILED ] HashTableTest.ForEach
1 FAILED TEST
FAIL hash_table_unittest (exit status: 1)
============================================================================
Testsuite summary for idba 1.1.3
============================================================================
# TOTAL: 12
# PASS: 11
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
============================================================================
See test/test-suite.log
Please report to loneknightpy@gmail.com
============================================================================
Makefile:891: recipe for target 'test-suite.log' failed
make[4]: *** [test-suite.log] Error 1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
Makefile:997: recipe for target 'check-TESTS' failed
make[3]: *** [check-TESTS] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
Makefile:1147: recipe for target 'check-am' failed
make[2]: *** [check-am] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
Makefile:357: recipe for target 'check-recursive' failed
make[1]: *** [check-recursive] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: make -j4 check VERBOSE=1 returned exit code 2
debian/rules:10: recipe for target 'build-arch' failed
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2017-06-17T23:07:00Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 0
Build-Time: 669
Distribution: stretch-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 203
Job: idba_1.1.3-1
Machine Architecture: armhf
Package: idba
Package-Time: 922
Source-Version: 1.1.3-1
Space: 0
Status: failed
Version: 1.1.3-1
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Finished at 2017-06-17T23:07:00Z
Build needed 00:00:00, 0k disc space