discosnp →
1.2.6-2 →
armhf → 2017-11-19 07:01:19
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| discosnp 1.2.6-2 (armhf) Sun, 19 Nov 2017 06:52:31 +0000 |
+==============================================================================+
Package: discosnp
Version: 1.2.6-2
Source Version: 1.2.6-2
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-fb671dda-e719-46db-95d6-0d86fc16fc30' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.4 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.2 MB]
Fetched 22.5 MB in 26s (849 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'discosnp' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/discosnp.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/discosnp.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 595 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main discosnp 1.2.6-2 (dsc) [2018 B]
Get:2 http://172.17.0.1/private buster-staging/main discosnp 1.2.6-2 (tar) [582 kB]
Get:3 http://172.17.0.1/private buster-staging/main discosnp 1.2.6-2 (diff) [11.3 kB]
Fetched 595 kB in 0s (2165 kB/s)
Download complete and in download only mode
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
I: NOTICE: Log filtering will replace 'build/discosnp-TqMHAP/discosnp-1.2.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/discosnp-TqMHAP' 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-FBMKci/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-FBMKci/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-FBMKci/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-FBMKci/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ Packages [432 B]
Fetched 2108 B in 0s (3076 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
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 48 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15098 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
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), bc, zlib1g-dev, help2man
Filtered Build-Depends: debhelper (>= 10), bc, zlib1g-dev, help2man
dpkg-deb: building package 'sbuild-build-depends-discosnp-dummy' in '/<<BUILDDIR>>/resolver-FBMKci/apt_archive/sbuild-build-depends-discosnp-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-discosnp-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-FBMKci/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ Sources [504 B]
Get:5 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ Packages [585 B]
Fetched 2422 B in 0s (3712 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: store: aptMethod::Configuration: could not load seccomp policy: Invalid argument
Reading package lists...
Install discosnp build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates e2fsprogs-l10n libsasl2-modules libssl1.1 openssl
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libreadline6
libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz 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 libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bc bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libfile-stripnondeterminism-perl libglib2.0-0 libicu57
liblocale-gettext-perl libmagic-mgc libmagic1 libpipeline1 libreadline6
libsigsegv2 libtimedate-perl libtool libxml2 m4 man-db po-debconf
sbuild-build-depends-discosnp-dummy zlib1g-dev
0 upgraded, 35 newly installed, 0 to remove and 48 not upgraded.
Need to get 19.2 MB of archives.
After this operation, 64.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-FBMKci/apt_archive ./ sbuild-build-depends-discosnp-dummy 0.invalid.0 [868 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf liblocale-gettext-perl armhf 1.07-3+b2 [18.3 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-3 [95.9 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.14 [178 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libreadline6 armhf 6.3-9 [122 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf bc armhf 1.06.95-9 [96.3 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.32-1 [225 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.32-1 [105 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.32-1 [63.7 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-4 [117 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-8 [7411 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-5 [609 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1+nmu1 [74.2 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-4 [434 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 15 [16.2 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.54.1-1 [2653 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-4 [1218 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.10.5 [978 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf help2man armhf 1.47.5 [162 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libarchive-zip-perl (1.59-1) ...
Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.54.1-1) ...
No schema files found: doing nothing.
Setting up gettext-base (0.19.8.1-4) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-8) ...
Setting up libbsd0:armhf (0.8.6-3) ...
Setting up libxml2:armhf (2.9.4+dfsg1-5) ...
Setting up libmagic-mgc (1:5.32-1) ...
Setting up libmagic1:armhf (1:5.32-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Processing triggers for libc-bin (2.24-17) ...
Setting up autotools-dev (20161112.1+nmu1) ...
Setting up liblocale-gettext-perl (1.07-3+b2) ...
Setting up bsdmainutils (9.0.14) ...
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 (0.19.8.1-4) ...
Setting up libreadline6:armhf (6.3-9) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.040-1) ...
Setting up gettext (0.19.8.1-4) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.32-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up help2man (1.47.5) ...
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up bc (1.06.95-9) ...
Setting up libtool (2.4.6-2) ...
Setting up po-debconf (1.0.20) ...
Setting up dh-autoreconf (15) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (10.10.5) ...
Setting up sbuild-build-depends-discosnp-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-17) ...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http: aptMethod::Configuration: could not load seccomp policy: Invalid argument
W: copy: aptMethod::Configuration: could not load seccomp policy: Invalid argument
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 3.19.0-trunk-armmp armhf (armv7l)
Toolchain package versions: binutils_2.29.1-6+rpi1 dpkg-dev_1.19.0.4 g++-7_7.2.0-12 gcc-7_7.2.0-12 libc6-dev_2.24-17 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 linux-libc-dev_4.9.51-1+rpi3+b1
Package versions: adduser_3.116 apt_1.6~alpha3 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-4 autotools-dev_20161112.1+nmu1 base-files_10+rpi1 base-passwd_3.5.44 bash_4.4-5 bc_1.06.95-9 binutils_2.29.1-6+rpi1 binutils-arm-linux-gnueabihf_2.29.1-6+rpi1 binutils-common_2.29.1-6+rpi1 bsdmainutils_9.0.14 bsdutils_1:2.30.2-0.1 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.11+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.2.0-12 dash_0.5.8-2.5 debconf_1.5.64 debhelper_10.10.5 debianutils_4.8.2 dh-autoreconf_15 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.1-5 dmsetup_2:1.02.142-1 dpkg_1.19.0.4 dpkg-dev_1.19.0.4 e2fslibs_1.43.7-1 e2fsprogs_1.43.7-1 e2fsprogs-l10n_1.43.7-1 fakeroot_1.22-1 fdisk_2.30.2-0.1 file_1:5.32-1 findutils_4.6.0+git+20170729-2 g++_4:7.2.0-1d1 g++-7_7.2.0-12 gcc_4:7.2.0-1d1 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-5-base_5.4.1-4 gcc-7_7.2.0-12 gcc-7-base_7.2.0-12 gettext_0.19.8.1-4 gettext-base_0.19.8.1-4 gnupg_2.2.1-5 gnupg-agent_2.2.1-5 gnupg-l10n_2.2.1-5 gnupg-utils_2.2.1-5 gpg_2.2.1-5 gpg-agent_2.2.1-5 gpg-wks-client_2.2.1-5 gpg-wks-server_2.2.1-5 gpgconf_2.2.1-5 gpgsm_2.2.1-5 gpgv_2.2.1-5 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 help2man_1.47.5 hostname_3.18 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libapparmor1_2.11.1-2 libapt-pkg5.0_1.6~alpha3 libarchive-zip-perl_1.59-1 libasan4_7.2.0-12 libassuan0_2.4.3-3 libatomic1_7.2.0-12 libattr1_1:2.4.47-2 libaudit-common_1:2.8.1-1 libaudit1_1:2.8.1-1 libbinutils_2.29.1-6+rpi1 libblkid1_2.30.2-0.1 libbsd0_0.8.6-3 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-17 libc-dev-bin_2.24-17 libc6_2.24-17 libc6-dev_2.24-17 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.1 libcc1-0_7.2.0-12 libcilkrts5_7.2.0-12 libcomerr2_1.43.7-1 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.11.22-1 libdebconfclient0_0.232 libdevmapper1.02.1_2:1.02.142-1 libdpkg-perl_1.19.0.4 libdrm-common_2.4.84-2+rpi1 libdrm2_2.4.84-2+rpi1 libfakeroot_1.22-1 libfdisk1_2.30.2-0.1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.2.0-12 libgcc1_1:7.2.0-12 libgcrypt20_1.7.9-1 libgdbm3_1.8.3-14 libglib2.0-0_2.54.1-1 libgmp10_2:6.1.2+dfsg-1.1 libgnutls30_3.5.16-1 libgomp1_7.2.0-12 libgpg-error0_1.27-4 libhogweed4_3.3-2 libicu57_57.1-8 libidn11_1.33-2 libidn2-0_2.0.2-5 libip4tc0_1.6.1-2+b1 libisl15_0.18-1 libklibc_2.0.4-9+rpi1 libkmod2_24-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-1 libmagic1_1:5.32-1 libmount1_2.30.2-0.1 libmpc3_1.0.3-2 libmpfr4_3.1.6-1 libncurses5_6.0+20170902-1 libncursesw5_6.0+20170902-1 libnettle6_3.3-2 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.9-2 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_2:8.39-4 libperl5.24_5.24.1-7 libperl5.26_5.26.1-2 libpipeline1_1.4.2-1 libplymouth4_0.9.3-1 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-3 libreadline6_6.3-9 libreadline7_7.0-3 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.11-1 libsmartcols1_2.30.2-0.1 libsqlite3-0_3.20.1-2 libss2_1.43.7-1 libssl1.1_1.1.0f-5 libstdc++-7-dev_7.2.0-12 libstdc++6_7.2.0-12 libsystemd0_235-2 libtasn1-6_4.12-2.1 libtimedate-perl_2.3000-2 libtinfo5_6.0+20170902-1 libtool_2.4.6-2 libubsan0_7.2.0-12 libudev1_235-2 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.30.2-0.1 libxml2_2.9.4+dfsg1-5 linux-base_4.5 linux-libc-dev_4.9.51-1+rpi3+b1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.30.2-0.1 mountall_2.54 multiarch-support_2.24-17 ncurses-base_6.0+20170902-1 ncurses-bin_6.0+20170902-1 openssl_1.1.0f-5 passwd_1:4.5-1 patch_2.7.5-1 perl_5.26.1-2 perl-base_5.26.1-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.1-2 pinentry-curses_1.0.0-3 plymouth_0.9.3-1 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-discosnp-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.10 systemd_235-2 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2017c-1 udev_235-2 util-linux_2.30.2-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_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 Tue Nov 14 09:09:00 2017 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./discosnp_1.2.6-2.dsc
dpkg-source: info: extracting discosnp in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking discosnp_1.2.6.orig.tar.gz
dpkg-source: info: unpacking discosnp_1.2.6-2.debian.tar.xz
dpkg-source: info: applying fix_build
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-fb671dda-e719-46db-95d6-0d86fc16fc30
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package discosnp
dpkg-buildpackage: info: source version 1.2.6-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build discosnp-1.2.6
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
debian/rules override_dh_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd minia && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/minia'
rm -rf *.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>/minia'
cd kissnp2 && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/kissnp2'
rm -rf *.o ../minia/*.o
make[2]: Leaving directory '/<<PKGBUILDDIR>>/kissnp2'
cd kissreads && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/kissreads'
rm -rf ./src/*.o kissreads
make[2]: Leaving directory '/<<PKGBUILDDIR>>/kissreads'
rm -f output_analyses/discoSnp_to_genotypes
rm -f output_analyses/discoSnp_to_csv
rm -f kissnp2/kissnp2
rm -f kissreads/kissreads
rm -f kissreads.1
rm -f kissnp2.1
dh_clean
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build
cd kissnp2 && make k=29
make[2]: Entering directory '/<<PKGBUILDDIR>>/kissnp2'
g++ -o ../minia/Pool.o -c ../minia/Pool.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o ../minia/Bank.o -c ../minia/Bank.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Bank.cpp: In member function 'void Bank::init(char**, int)':
../minia/Bank.cpp:279:19: warning: ignoring return value of 'char* strerror_r(int, char*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
strerror_r( errno, buffer, BUFSIZ ); // get string message from errno
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../minia/Bank.cpp: In member function 'void BinaryBank::open(bool)':
../minia/Bank.cpp:710:19: warning: ignoring return value of 'char* strerror_r(int, char*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
strerror_r( errno, buffer, BUFSIZ ); // get string message from errno
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../minia/Bank.cpp: In member function 'void BinaryReads::open(bool)':
../minia/Bank.cpp:795:19: warning: ignoring return value of 'char* strerror_r(int, char*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
strerror_r( errno, buffer, BUFSIZ ); // get string message from errno
~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
../minia/Bank.cpp: In member function 'int KmersBuffer::readkmers()':
../minia/Bank.cpp:985:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(buffer,sizeof( char),block_size, binary_read_file); // read a block of sequences into the buffer
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o ../minia/Bloom.o -c ../minia/Bloom.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Bloom.cpp: In member function 'void Bloom::load(char*)':
../minia/Bloom.cpp:257:7: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(blooma, sizeof(unsigned char), nchar, file_data);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o ../minia/Hash16.o -c ../minia/Hash16.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o ../minia/Terminator.o -c ../minia/Terminator.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Terminator.cpp: In constructor 'BranchingTerminator::BranchingTerminator(BinaryBank*, BinaryBank*, Bloom*, Set*)':
../minia/Terminator.cpp:337:186: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=]
fprintf (stderr,"\nLoaded %lld branching kmers x %lu B = %.1f MB\n",nb_branching_kmers,sizeof(cell<kmer_type>),((1<<NBITS_TERMINATOR)*sizeof(cell<kmer_type>)*1.0)/1024.0/1024.0);
^
g++ -o ../minia/Kmer.o -c ../minia/Kmer.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o ../minia/Traversal.o -c ../minia/Traversal.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Traversal.cpp: In member function 'bool MonumentTraversal::find_starting_kmer(kmer_type, kmer_type&)':
../minia/Traversal.cpp:352:252: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'std::set<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
if (debug) printf("depth %d useless int %d and starting belongs %d nb involved nodes %lu\n",frontline.depth,useless_int,all_involved_extensions.find(starting_kmer) != all_involved_extensions.end(),all_involved_extensions.size());
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
../minia/Traversal.cpp: In member function 'bool MonumentTraversal::validate_consensuses(std::set<std::__cxx11::basic_string<char> >, char*, int&)':
../minia/Traversal.cpp:820:101: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::__cxx11::basic_string<char>::size_type {aka unsigned int}' [-Wformat=]
if (debug) printf("bubble path %d: %s (len=%lu)\n",path_number,(*it).c_str(),(*it).length());
~~~~~~~~~~~~~~^
../minia/Traversal.cpp:841:87: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::set<std::__cxx11::basic_string<char> >::size_type {aka unsigned int}' [-Wformat=]
if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev);
~~~~~~~~~~~~~~~~~~ ^
In file included from /usr/include/c++/7/deque:66:0,
from /usr/include/c++/7/queue:60,
from ../minia/Traversal.h:5,
from ../minia/Traversal.cpp:3:
/usr/include/c++/7/bits/deque.tcc: In function 'std::_Deque_iterator<_Tp, _Tp&, _Tp*> std::copy(std::_Deque_iterator<_Tp, const _Tp&, const _Tp*>, std::_Deque_iterator<_Tp, const _Tp&, const _Tp*>, std::_Deque_iterator<_Tp, _Tp&, _Tp*>) [with _Tp = kmer_strand_nt]':
/usr/include/c++/7/bits/deque.tcc:985:5: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
copy(_Deque_iterator<_Tp, const _Tp&, const _Tp*> __first,
^~~~
/usr/include/c++/7/bits/deque.tcc:985:5: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc: In member function 'void std::deque<_Tp, _Alloc>::_M_insert_aux(std::deque<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::deque<_Tp, _Alloc>::size_type) [with _ForwardIterator = std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>; _Tp = kmer_strand_nt; _Alloc = std::allocator<kmer_strand_nt>]':
/usr/include/c++/7/bits/deque.tcc:757:7: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
deque<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/deque.tcc:757:7: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
In file included from /usr/include/c++/7/deque:64:0,
from /usr/include/c++/7/queue:60,
from ../minia/Traversal.h:5,
from ../minia/Traversal.cpp:3:
/usr/include/c++/7/bits/stl_deque.h:429:18: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
__result); }
^
/usr/include/c++/7/bits/stl_deque.h:429:18: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_deque.h:429:18: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
In file included from /usr/include/c++/7/deque:66:0,
from /usr/include/c++/7/queue:60,
from ../minia/Traversal.h:5,
from ../minia/Traversal.cpp:3:
/usr/include/c++/7/bits/deque.tcc:780:7: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
std::copy(__first, __last, __pos - difference_type(__n));
^~~
/usr/include/c++/7/bits/deque.tcc:780:7: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:780:7: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:791:7: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
std::copy(__mid, __last, __old_start);
^~~
/usr/include/c++/7/bits/deque.tcc:791:7: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:791:7: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:820:5: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
std::copy(__first, __last, __pos);
^~~
/usr/include/c++/7/bits/deque.tcc:820:5: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:820:5: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:831:5: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
std::copy(__first, __mid, __pos);
^~~
/usr/include/c++/7/bits/deque.tcc:831:5: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:831:5: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc: In member function 'std::deque<_Tp, _Alloc>& std::deque<_Tp, _Alloc>::operator=(const std::deque<_Tp, _Alloc>&) [with _Tp = kmer_strand_nt; _Alloc = std::allocator<kmer_strand_nt>]':
/usr/include/c++/7/bits/deque.tcc:116:21: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
_M_erase_at_end(std::copy(__x.begin(), __x.end(),
~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
this->_M_impl._M_start));
~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/deque.tcc:116:21: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:116:21: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:121:8: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
std::copy(__x.begin(), __mid, this->_M_impl._M_start);
^~~
/usr/include/c++/7/bits/deque.tcc:121:8: note: parameter passing for argument of type 'std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>' changed in GCC 7.1
/usr/include/c++/7/bits/deque.tcc:121:8: note: parameter passing for argument of type 'std::deque<kmer_strand_nt, std::allocator<kmer_strand_nt> >::const_iterator {aka std::_Deque_iterator<kmer_strand_nt, const kmer_strand_nt&, const kmer_strand_nt*>}' changed in GCC 7.1
g++ -o ../minia/LinearCounter.o -c ../minia/LinearCounter.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o ../minia/Set.o -c ../minia/Set.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Set.cpp: In member function 'void AssocSet::print_total_size()':
../minia/Set.cpp:132:48: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("Assoc set size: %li\n",liste.size());
~~~~~~~~~~~~^
../minia/Set.cpp:133:103: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("Assoc set capacity: listekmer %li liste val%li\n",liste.capacity(),liste_value.capacity());
~~~~~~~~~~~~~~~~ ^
../minia/Set.cpp:133:103: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'std::vector<short unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:134:48:
printf("%li *%li + %li* %li = %li MB \n",liste.capacity(),sizeof(set_elem),liste_value.capacity(),sizeof(set_value_t),
~~~~~~~~~~~~~~~~
../minia/Set.cpp:136:11:
);
^
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'std::vector<short unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:136:11: warning: format '%li' expects argument of type 'long int', but argument 6 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp: In member function 'void AssocPairedSet::print()':
../minia/Set.cpp:242:45: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("print %lu elems \n",liste.size());
~~~~~~~~~~~~^
../minia/Set.cpp: In member function 'void AssocPairedSet::print_total_size()':
../minia/Set.cpp:298:55: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("Assoc paired set size: %li\n",liste.size());
~~~~~~~~~~~~^
../minia/Set.cpp:299:110: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
printf("Assoc paired set capacity: listekmer %li liste val%li\n",liste.capacity(),liste_value.capacity());
~~~~~~~~~~~~~~~~ ^
../minia/Set.cpp:299:110: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'std::vector<pair_nt_kmer>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:302:12: warning: format '%li' expects argument of type 'long int', but argument 2 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:300:48:
printf("%li *%li + %li* %li = %li MB \n",liste.capacity(),sizeof(set_elem),liste_value.capacity(),sizeof(set_value_t),
~~~~~~~~~~~~~~~~
../minia/Set.cpp:302:12:
);
^
../minia/Set.cpp:302:12: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:302:12: warning: format '%li' expects argument of type 'long int', but argument 4 has type 'std::vector<pair_nt_kmer>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp:302:12: warning: format '%li' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:302:12: warning: format '%li' expects argument of type 'long int', but argument 6 has type 'std::vector<long long unsigned int>::size_type {aka unsigned int}' [-Wformat=]
../minia/Set.cpp: In member function 'void AssocPairedSet::load(char*)':
../minia/Set.cpp:290:10: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&liste_value[0], sizeof(pair_nt_kmer_t), liste_value.size(), file_data);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../minia/Set.h:10,
from ../minia/Set.cpp:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../minia/Set.h:10,
from ../minia/Set.cpp:1:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void AssocPairedSet::load_branching(BinaryBank*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../minia/Pool.h:11,
from ../minia/Hash16.h:12,
from ../minia/Set.h:6,
from ../minia/Set.cpp:1:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../minia/Pool.h:11,
from ../minia/Hash16.h:12,
from ../minia/Set.h:6,
from ../minia/Set.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual void AssocPairedSet::finalize()':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual void ListSet::finalize()':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'virtual void AssocSet::finalize()':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
g++ -o ../minia/Utils.o -c ../minia/Utils.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Utils.cpp: In function 'void end_kmer_count_partition(bool, Hash16*)':
../minia/Utils.cpp:187:14: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(F_kmercpt_write), 0); //erase previous file
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
../minia/Utils.cpp:199:14: warning: ignoring return value of 'size_t fread(void*, size_t, size_t, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
fread(&cptk, sizeof(cptk), 1, F_kmercpt_read);
~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../minia/Utils.cpp:225:18: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(F_kmercpt_read), 0); //erase previous file
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o ../minia/SortingCount.o -c ../minia/SortingCount.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/SortingCount.cpp: In function 'void sorting_count(Bank*, char*, int, int, bool, int, bool)':
../minia/SortingCount.cpp:56:15: warning: ignoring return value of 'char* getcwd(char*, size_t)', declared with attribute warn_unused_result [-Wunused-result]
getcwd(current_path,sizeof(current_path));
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../minia/SortingCount.cpp:283:15: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system("echo 3 > /proc/sys/vm/drop_caches");
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../minia/SortingCount.cpp:537:19: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system("echo 3 > /proc/sys/vm/drop_caches");
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../minia/SortingCount.h:8,
from ../minia/SortingCount.cpp:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator {aka __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../minia/Utils.h:9,
from ../minia/SortingCount.h:17,
from ../minia/SortingCount.cpp:1:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Distance = int; _Tp = long long unsigned int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../minia/Utils.h:9,
from ../minia/SortingCount.h:17,
from ../minia/SortingCount.cpp:1:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../minia/SortingCount.h:8,
from ../minia/SortingCount.cpp:1:
/usr/include/c++/7/bits/stl_vector.h: In function 'void sorting_count(Bank*, char*, int, int, bool, int, bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../minia/Utils.h:9,
from ../minia/SortingCount.h:17,
from ../minia/SortingCount.cpp:1:
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
g++ -o ../minia/Debloom.o -c ../minia/Debloom.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Debloom.cpp: In function 'void end_debloom_partition(bool)':
../minia/Debloom.cpp:29:11: warning: ignoring return value of 'int ftruncate(int, __off_t)', declared with attribute warn_unused_result [-Wunused-result]
ftruncate(fileno(F_debloom_write), 0); //erase previous file
~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o ../minia/OAHash.o -c ../minia/OAHash.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o Kmer_for_kissnp2.o -c Kmer_for_kissnp2.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o SNP.o -c SNP.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
SNP.cpp: In member function 'void Bubble::find_bubbles(const char*, int, int)':
SNP.cpp:858:49: warning: format '%llu' expects argument of type 'long long unsigned int', but argument 3 has type 'long unsigned int' [-Wformat=]
{printf("%c \t %llu %%",13,(nb*100)/nbel);
~~~~~~~~~~~~~^
g++ -o filter.o -c filter.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o IterativeExtensions.o -c IterativeExtensions.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
IterativeExtensions.cpp: In static member function 'static void IterativeExtensions::construct_linear_seqs(std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string, int, int, parcours_t, bool)':
IterativeExtensions.cpp:237:126: warning: format '%d' expects argument of type 'int', but argument 3 has type 'long long int' [-Wformat=]
printf("... XXX Stopped extending node %s because %d nodes reached. Was at depth %d.\n", node, nbNodes, depth);
^
In file included from /usr/include/c++/7/vector:69:0,
from ../minia/Set.h:10,
from ../minia/Terminator.h:13,
from IterativeExtensions.h:42,
from IterativeExtensions.cpp:37:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const kmer_strand_depth&}; _Tp = kmer_strand_depth; _Alloc = std::allocator<kmer_strand_depth>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<kmer_strand_depth>::iterator {aka __gnu_cxx::__normal_iterator<kmer_strand_depth*, std::vector<kmer_strand_depth> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../minia/Set.h:10,
from ../minia/Terminator.h:13,
from IterativeExtensions.h:42,
from IterativeExtensions.cpp:37:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void IterativeExtensions::construct_linear_seqs(std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string, int, int, parcours_t, bool)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<kmer_strand_depth*, std::vector<kmer_strand_depth> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../minia/Set.h:10,
from ../minia/Terminator.h:13,
from IterativeExtensions.h:42,
from IterativeExtensions.cpp:37:
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<kmer_strand_depth*, std::vector<kmer_strand_depth> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../minia/Set.h:10,
from ../minia/Terminator.h:13,
from IterativeExtensions.h:42,
from IterativeExtensions.cpp:37:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void IterativeExtensions::construct_linear_seqs_paired(std::__cxx11::string, std::__cxx11::string, int, std::__cxx11::string, int, int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<kmer_strand_depth*, std::vector<kmer_strand_depth> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../minia/Set.h:10,
from ../minia/Terminator.h:13,
from IterativeExtensions.h:42,
from IterativeExtensions.cpp:37:
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<kmer_strand_depth*, std::vector<kmer_strand_depth> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<kmer_strand_depth*, std::vector<kmer_strand_depth> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../minia/Set.h:10,
from ../minia/Terminator.h:13,
from IterativeExtensions.h:42,
from IterativeExtensions.cpp:37:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void IterativeExtensions::construct_linear_seqs(std::__cxx11::string, int, std::__cxx11::string)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<kmer_strand_depth*, std::vector<kmer_strand_depth> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../minia/Set.h:10,
from ../minia/Terminator.h:13,
from IterativeExtensions.h:42,
from IterativeExtensions.cpp:37:
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<kmer_strand_depth*, std::vector<kmer_strand_depth> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o commons.o -c commons.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o kissnp2 ../minia/Pool.o ../minia/Bank.o ../minia/Bloom.o ../minia/Hash16.o ../minia/Terminator.o ../minia/Kmer.o ../minia/Traversal.o ../minia/LinearCounter.o ../minia/Set.o ../minia/Utils.o ../minia/SortingCount.o ../minia/Debloom.o ../minia/OAHash.o Kmer_for_kissnp2.o SNP.o filter.o IterativeExtensions.o commons.o kissnp2.cpp -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissnp2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -Wl,-z,relro
kissnp2.cpp: In function 'int main(int, char**)':
kissnp2.cpp:256:85: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'unsigned int' [-Wformat=]
printf("Max kmer size on this compiled version is %lu\n",sizeof(kmer_type)*2);
^
make[2]: Leaving directory '/<<PKGBUILDDIR>>/kissnp2'
cd kissreads && make k=29
make[2]: Entering directory '/<<PKGBUILDDIR>>/kissreads'
gcc -o src/coherent_algorithm.o -c src/coherent_algorithm.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/commons.o -c src/commons.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/couple.o -c src/couple.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/extension_algorithm.o -c src/extension_algorithm.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
src/extension_algorithm.c: In function 'read_coherence':
src/extension_algorithm.c:312:23: warning: unused variable 'j' [-Wunused-variable]
int read_len, i, ii, j, starter_id, pwi, stop, read_coherence;
^
gcc -o src/fragment_index.o -c src/fragment_index.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
src/fragment_index.c: In function 'index_starters_from_input_file':
src/fragment_index.c:148:7: warning: unused variable 'validSeed' [-Wunused-variable]
char validSeed;
^~~~~~~~~
src/fragment_index.c:147:8: warning: unused variable 'j' [-Wunused-variable]
int i,j,z,stop;
^
gcc -o src/kissReads.o -c src/kissReads.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/list.o -c src/list.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/outputs.o -c src/outputs.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/interface_libchash.o -c src/interface_libchash.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
gcc -o src/libchash.o -c src/libchash.c -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -I./include/
In file included from src/libchash.c:126:0:
src/libchash.c: In function 'EntriesUpto':
src/libchash.c:468:14: warning: comparison with string literal results in unspecified behavior [-Waddress]
assert("" == "word size is too big in EntriesUpto()");
^
src/libchash.c: In function 'Delete':
src/libchash.c:165:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if ( STORES_PTR(ht) && (ht)->fSaveKeys ) \
^
./include/libchash.h:165:40: note: in expansion of macro 'FREE_KEY'
FREE_KEY(ht, (bck)->key); } while ( 0 )
^~~~~~~~
src/libchash.c:1119:4: note: in expansion of macro 'SET_BCK_DELETED'
SET_BCK_DELETED(ht, ht->posLastFind); /* find set this, how nice */
^~~~~~~~~~~~~~~
src/libchash.c: In function 'ClearHashTable':
src/libchash.c:165:7: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if ( STORES_PTR(ht) && (ht)->fSaveKeys ) \
^
src/libchash.c:1183:3: note: in expansion of macro 'FREE_KEY'
FREE_KEY(ht, bck->key);
^~~~~~~~
src/libchash.c: In function 'HashFirstBucket':
src/libchash.c:1289:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if ( !IS_BCK_DELETED(retval) )
^
src/libchash.c: In function 'HashNextBucket':
src/libchash.c:1299:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if ( !IS_BCK_DELETED(retval) )
^
src/libchash.c: In function 'HashDoLoad':
src/libchash.c:1431:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wdangling-else]
if ( dataRead != NULL ) /* if it's null, we're done */
^
src/libchash.c: In function 'HashFind':
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:220:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^~~~~~~
src/libchash.c:1221:4: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL));
^~~~~~~~~~~~~~~
src/libchash.c: In function 'HashFindLast':
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:220:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^~~~~~~
src/libchash.c:1226:4: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, ht->posLastFind);
^~~~~~~~~~~~~~~
src/libchash.c: In function 'HashFirstBucket':
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:220:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^~~~~~~
src/libchash.c:1290:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, retval);
^~~~~~~~~~~~~~~
src/libchash.c: In function 'HashNextBucket':
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:220:7: note: in expansion of macro 'READ_UL'
READ_UL((ht)->fpData, cchData); \
^~~~~~~
src/libchash.c:1300:3: note: in expansion of macro 'LOAD_AND_RETURN'
LOAD_AND_RETURN(ht, retval);
^~~~~~~~~~~~~~~
src/libchash.c: In function 'HashDoLoad':
src/libchash.c:1407:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(szMagicKey, 1, 4, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:1416:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cchKey);
^~~~~~~
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:1417:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cItems);
^~~~~~~
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:1418:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, ht->cDeletedItems);
^~~~~~~
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:1421:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, cchKey);
^~~~~~~
src/libchash.c:1423:4: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(rgchKeys, 1, cchKey, fp);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:1428:7: note: in expansion of macro 'READ_UL'
READ_UL(fp, bck->data); /* all we need if dataRead is NULL */
^~~~~~~
src/libchash.c: In function 'SparseRead':
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:622:4: note: in expansion of macro 'READ_UL'
READ_UL(fp, cBuckets); /* actually, cBuckets is stored */
^~~~~~~
src/libchash.c:193:7: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(&_ul, sizeof(_ul), 1, (fp)); \
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
src/libchash.c:627:3: note: in expansion of macro 'READ_UL'
READ_UL(fp, (*pbinSparse)[i].bmOccupied[j]);
^~~~~~~
At top level:
src/libchash.c:789:14: warning: 'DenseMemory' defined but not used [-Wunused-function]
static ulong DenseMemory(ulong cBuckets, ulong cOccupied)
^~~~~~~~~~~
src/libchash.c:767:14: warning: 'DenseRead' defined but not used [-Wunused-function]
static ulong DenseRead(FILE *fp, DenseBin **pbin)
^~~~~~~~~
src/libchash.c:748:13: warning: 'DenseWrite' defined but not used [-Wunused-function]
static void DenseWrite(FILE *fp, DenseBin *bin, ulong cBuckets)
^~~~~~~~~~
src/libchash.c:739:21: warning: 'DenseFirstBucket' defined but not used [-Wunused-function]
static DenseBucket *DenseFirstBucket(DenseIterator *iter,
^~~~~~~~~~~~~~~~
src/libchash.c:710:21: warning: 'DenseInsert' defined but not used [-Wunused-function]
static DenseBucket *DenseInsert(DenseBin *bin, DenseBucket *bckInsert,
^~~~~~~~~~~
src/libchash.c:691:18: warning: 'DenseFree' defined but not used [-Wunused-function]
static DenseBin *DenseFree(DenseBin *bin, ulong cBuckets)
^~~~~~~~~
gcc -o kissreads src/coherent_algorithm.o src/commons.o src/couple.o src/extension_algorithm.o src/fragment_index.o src/kissReads.o src/list.o src/outputs.o src/interface_libchash.o src/libchash.o -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>/kissreads=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -lz -Wl,-z,relro -Wall -lm -O3 -lz
#################
# Compilation OK#
#################
make[2]: Leaving directory '/<<PKGBUILDDIR>>/kissreads'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cp output_analyses/discoSnp_to_genotypes.py output_analyses/discoSnp_to_genotypes
cp output_analyses/discoSnp_to_csv.py output_analyses/discoSnp_to_csv
help2man --help-option=-h --no-discard-stderr --version-string=1.2.6 kissnp2/kissnp2 > kissnp2.1
help2man --help-option=-h --no-discard-stderr --version-string=1.2.6 kissreads/kissreads > kissreads.1
dh_install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/discosnp/usr/bin/kissnp2 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/discosnp/usr/bin/kissnp2 debian/discosnp/usr/bin/kissreads were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'discosnp-dbgsym' in '../discosnp-dbgsym_1.2.6-2_armhf.deb'.
dpkg-deb: building package 'discosnp' in '../discosnp_1.2.6-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../discosnp_1.2.6-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build discosnp-1.2.6
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-11-19T07:00:36Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
discosnp_1.2.6-2_armhf.changes:
-------------------------------
Format: 1.8
Date: Tue, 14 Nov 2017 10:05:31 +0100
Source: discosnp
Binary: discosnp
Architecture: armhf
Version: 1.2.6-2
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
discosnp - discovering Single Nucleotide Polymorphism from raw set(s) of rea
Changes:
discosnp (1.2.6-2) unstable; urgency=medium
.
* Secure URI in watch file
* Mention that program is superseded by DiscoSnp++
* Moved packaging from SVN to Git
* debhelper 10
* d/rules: do not parse d/changelog
* Standards-Version: 4.1.1
* DEP5
* Remove unused lintian override
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Checksums-Sha256:
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Files:
f888da096b2b1b4d4a4d4aaeb24abf52 558116 debug optional discosnp-dbgsym_1.2.6-2_armhf.deb
a6e5c50f1e2bab8be2c226e781040854 4505 science optional discosnp_1.2.6-2_armhf.buildinfo
39278c70af5f0cd1d82da0a4aec99bcd 125852 science optional discosnp_1.2.6-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
discosnp-dbgsym_1.2.6-2_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 558116 bytes: control archive=596 bytes.
415 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: discosnp-dbgsym
Source: discosnp
Version: 1.2.6-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 598
Depends: discosnp (= 1.2.6-2)
Section: debug
Priority: optional
Description: debug symbols for discosnp
Build-Ids: 8c359e6491d8392cd7f93cb4164ff97a3b284f5a c772116b9a6c962a4615a8d2be2d0e9541207cc8
drwxr-xr-x root/root 0 2017-11-14 09:05 ./
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/lib/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/lib/debug/.build-id/8c/
-rw-r--r-- root/root 84448 2017-11-14 09:05 ./usr/lib/debug/.build-id/8c/359e6491d8392cd7f93cb4164ff97a3b284f5a.debug
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/lib/debug/.build-id/c7/
-rw-r--r-- root/root 515220 2017-11-14 09:05 ./usr/lib/debug/.build-id/c7/72116b9a6c962a4615a8d2be2d0e9541207cc8.debug
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-11-14 09:05 ./usr/share/doc/discosnp-dbgsym -> discosnp
discosnp_1.2.6-2_armhf.deb
--------------------------
new Debian package, version 2.0.
size 125852 bytes: control archive=1280 bytes.
1095 bytes, 26 lines control
850 bytes, 12 lines md5sums
Package: discosnp
Version: 1.2.6-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 280
Depends: libc6 (>= 2.4), libgcc1 (>= 1:3.5), libstdc++6 (>= 5.2), zlib1g (>= 1:1.2.3.4), bc, python
Section: science
Priority: optional
Homepage: http://colibread.inria.fr/discosnp/
Description: discovering Single Nucleotide Polymorphism from raw set(s) of reads
Software discoSnp is designed for discovering Single Nucleotide
Polymorphism (SNP) from raw set(s) of reads obtained with Next Generation
Sequencers (NGS).
.
Note that number of input read sets is not constrained, it can be one, two,
or more. Note also that no other data as reference genome or annotations
are needed.
.
The software is composed by two modules. First module, kissnp2, detects SNPs
from read sets. A second module, kissreads, enhance the kissnp2 results by
computing per read set and for each found SNP:
.
1) its mean read coverage
2) the (phred) quality of reads generating the polymorphism.
.
This program is superseded by DiscoSnp++.
drwxr-xr-x root/root 0 2017-11-14 09:05 ./
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/bin/
-rwxr-xr-x root/root 1612 2017-11-14 09:05 ./usr/bin/discoSnp_to_csv
-rwxr-xr-x root/root 2099 2017-11-14 09:05 ./usr/bin/discoSnp_to_genotypes
-rwxr-xr-x root/root 149568 2017-11-14 09:05 ./usr/bin/kissnp2
-rwxr-xr-x root/root 54968 2017-11-14 09:05 ./usr/bin/kissreads
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/discosnp/
-rw-r--r-- root/root 465 2017-11-14 09:05 ./usr/share/doc/discosnp/README.Debian
-rw-r--r-- root/root 4896 2014-07-28 15:18 ./usr/share/doc/discosnp/README.txt.gz
-rw-r--r-- root/root 594 2017-11-14 09:05 ./usr/share/doc/discosnp/changelog.Debian.gz
-rw-r--r-- root/root 25363 2017-11-14 09:05 ./usr/share/doc/discosnp/copyright
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/discosnp/examples/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/doc/discosnp/examples/data_sample/
-rw-r--r-- root/root 12531 2013-10-14 18:51 ./usr/share/doc/discosnp/examples/data_sample/reads_sequence1.fasta.gz
-rw-r--r-- root/root 13427 2017-11-14 09:05 ./usr/share/doc/discosnp/examples/data_sample/reads_sequence2.fasta.gz
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/man/
drwxr-xr-x root/root 0 2017-11-14 09:05 ./usr/share/man/man1/
-rw-r--r-- root/root 1273 2017-11-14 09:05 ./usr/share/man/man1/kissnp2.1.gz
-rw-r--r-- root/root 1407 2017-11-14 09:05 ./usr/share/man/man1/kissreads.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 7960
Build-Time: 223
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 210
Job: discosnp_1.2.6-2
Machine Architecture: armhf
Package: discosnp
Package-Time: 485
Source-Version: 1.2.6-2
Space: 7960
Status: successful
Version: 1.2.6-2
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Finished at 2017-11-19T07:00:36Z
Build needed 00:08:05, 7960k disc space