Raspbian Package Auto-Building

Build log for discosnp (1.2.2-1) on armhf

discosnp1.2.2-1armhf → 2014-06-04 05:33:09

sbuild (Debian sbuild) 0.63.2 (18 Aug 2012) on bm-wb-01

╔══════════════════════════════════════════════════════════════════════════════╗
║ discosnp 1.2.2-1 (armhf)                                   04 Jun 2014 05:26 ║
╚══════════════════════════════════════════════════════════════════════════════╝

Package: discosnp
Version: 1.2.2-1
Source Version: 1.2.2-1
Distribution: jessie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'build/discosnp-Et96bl/discosnp-1.2.2' with '«PKGBUILDDIR»'
I: NOTICE: Log filtering will replace 'build/discosnp-Et96bl' with '«BUILDDIR»'
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/jessie-staging-armhf-sbuild-20bf2ba7-0f99-47a8-9a85-88bc439310b7' with '«CHROOT»'

┌──────────────────────────────────────────────────────────────────────────────┐
│ Update chroot                                                                │
└──────────────────────────────────────────────────────────────────────────────┘

Get:1 http://172.17.0.1 jessie-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1 jessie-staging/main Sources [7298 kB]
Get:3 http://172.17.0.1 jessie-staging/main armhf Packages [8126 kB]
Ign http://172.17.0.1 jessie-staging/main Translation-en
Fetched 15.4 MB in 28s (546 kB/s)
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Fetch source files                                                           │
└──────────────────────────────────────────────────────────────────────────────┘


Check APT
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Checking available source versions...

Download source files with APT
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Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'discosnp' packaging is maintained in the 'Svn' version control system at:
svn://anonscm.debian.org/debian-med/trunk/packages/discosnp/trunk/
Need to get 576 kB of source archives.
Get:1 http://172.17.0.1/private/ jessie-staging/main discosnp 1.2.2-1 (dsc) [1996 B]
Get:2 http://172.17.0.1/private/ jessie-staging/main discosnp 1.2.2-1 (tar) [562 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main discosnp 1.2.2-1 (diff) [11.3 kB]
Fetched 576 kB in 0s (4160 kB/s)
Download complete and in download only mode

Check arch
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Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package `sbuild-build-depends-core-dummy' in `/«BUILDDIR»/resolver-nxGyTk/apt_archive/sbuild-build-depends-core-dummy.deb'.
OK
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Install core build dependencies (apt-based resolver)                         │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
debconf: delaying package configuration, since apt-utils is not installed
0 upgraded, 1 newly installed, 0 to remove and 48 not upgraded.
Need to get 0 B/818 B of archives.
After this operation, 0 B of additional disk space will be used.
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11664 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Merged Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev | libc-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bc, zlib1g-dev, help2man
Filtered Build-Depends: base-files, base-passwd, bash, bsdutils, coreutils, dash, debianutils, diffutils, dpkg, e2fsprogs, findutils, grep, gzip, hostname, libc-bin, login, mount, ncurses-base, ncurses-bin, perl-base, sed, sysvinit, sysvinit-utils, tar, util-linux, libc6-dev, gcc (>= 4:4.4.3), g++ (>= 4:4.4.3), make, dpkg-dev (>= 1.13.5), debhelper (>= 9), bc, zlib1g-dev, help2man
dpkg-deb: building package `sbuild-build-depends-discosnp-dummy' in `/«BUILDDIR»/resolver-o5qQOo/apt_archive/sbuild-build-depends-discosnp-dummy.deb'.
OK
Reading package lists...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Install discosnp build dependencies (apt-based resolver)                     │
└──────────────────────────────────────────────────────────────────────────────┘

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  bc bsdmainutils debhelper file gettext gettext-base groff-base help2man
  install-info intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0
  libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf zlib1g-dev
Suggested packages:
  wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
  libmail-box-perl
Recommended packages:
  curl wget lynx-cur autopoint libasprintf-dev libgettextpo-dev
  libglib2.0-data shared-mime-info xml-core libmail-sendmail-perl
The following NEW packages will be installed:
  bc bsdmainutils debhelper file gettext gettext-base groff-base help2man
  install-info intltool-debian libasprintf0c2 libcroco3 libffi6 libglib2.0-0
  libmagic1 libpipeline1 libunistring0 libxml2 man-db po-debconf
  sbuild-build-depends-discosnp-dummy zlib1g-dev
0 upgraded, 22 newly installed, 0 to remove and 48 not upgraded.
Need to get 8895 kB/8896 kB of archives.
After this operation, 23.8 MB of additional disk space will be used.
Get:1 http://172.17.0.1/private/ jessie-staging/main install-info armhf 5.2.0.dfsg.1-3 [191 kB]
Get:2 http://172.17.0.1/private/ jessie-staging/main libpipeline1 armhf 1.3.0-1 [21.1 kB]
Get:3 http://172.17.0.1/private/ jessie-staging/main groff-base armhf 1.22.2-5 [962 kB]
Get:4 http://172.17.0.1/private/ jessie-staging/main bsdmainutils armhf 9.0.5 [206 kB]
Get:5 http://172.17.0.1/private/ jessie-staging/main man-db armhf 2.6.7.1-1 [964 kB]
Get:6 http://172.17.0.1/private/ jessie-staging/main libasprintf0c2 armhf 0.18.3.2-1 [29.0 kB]
Get:7 http://172.17.0.1/private/ jessie-staging/main libmagic1 armhf 1:5.18-1 [229 kB]
Get:8 http://172.17.0.1/private/ jessie-staging/main libxml2 armhf 2.9.1+dfsg1-3 [836 kB]
Get:9 http://172.17.0.1/private/ jessie-staging/main libffi6 armhf 3.1~rc1+r3.0.13-12 [17.6 kB]
Get:10 http://172.17.0.1/private/ jessie-staging/main libglib2.0-0 armhf 2.40.0-3 [2247 kB]
Get:11 http://172.17.0.1/private/ jessie-staging/main libcroco3 armhf 0.6.8-2 [119 kB]
Get:12 http://172.17.0.1/private/ jessie-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:13 http://172.17.0.1/private/ jessie-staging/main bc armhf 1.06.95-8 [106 kB]
Get:14 http://172.17.0.1/private/ jessie-staging/main file armhf 1:5.18-1 [57.2 kB]
Get:15 http://172.17.0.1/private/ jessie-staging/main gettext-base armhf 0.18.3.2-1 [112 kB]
Get:16 http://172.17.0.1/private/ jessie-staging/main gettext armhf 0.18.3.2-1 [1137 kB]
Get:17 http://172.17.0.1/private/ jessie-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:18 http://172.17.0.1/private/ jessie-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:19 http://172.17.0.1/private/ jessie-staging/main debhelper all 9.20140228 [691 kB]
Get:20 http://172.17.0.1/private/ jessie-staging/main help2man armhf 1.45.1 [95.8 kB]
Get:21 http://172.17.0.1/private/ jessie-staging/main zlib1g-dev armhf 1:1.2.8.dfsg-1 [212 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 8895 kB in 2s (4307 kB/s)
Selecting previously unselected package install-info.
(Reading database ... 11664 files and directories currently installed.)
Preparing to unpack .../install-info_5.2.0.dfsg.1-3_armhf.deb ...
Unpacking install-info (5.2.0.dfsg.1-3) ...
Setting up install-info (5.2.0.dfsg.1-3) ...
Selecting previously unselected package libpipeline1:armhf.
(Reading database ... 11678 files and directories currently installed.)
Preparing to unpack .../libpipeline1_1.3.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.3.0-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../groff-base_1.22.2-5_armhf.deb ...
Unpacking groff-base (1.22.2-5) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../bsdmainutils_9.0.5_armhf.deb ...
Unpacking bsdmainutils (9.0.5) ...
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Preparing to unpack .../man-db_2.6.7.1-1_armhf.deb ...
Unpacking man-db (2.6.7.1-1) ...
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Preparing to unpack .../libasprintf0c2_0.18.3.2-1_armhf.deb ...
Unpacking libasprintf0c2:armhf (0.18.3.2-1) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../libmagic1_1%3a5.18-1_armhf.deb ...
Unpacking libmagic1:armhf (1:5.18-1) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../libxml2_2.9.1+dfsg1-3_armhf.deb ...
Unpacking libxml2:armhf (2.9.1+dfsg1-3) ...
Selecting previously unselected package libffi6:armhf.
Preparing to unpack .../libffi6_3.1~rc1+r3.0.13-12_armhf.deb ...
Unpacking libffi6:armhf (3.1~rc1+r3.0.13-12) ...
Selecting previously unselected package libglib2.0-0:armhf.
Preparing to unpack .../libglib2.0-0_2.40.0-3_armhf.deb ...
Unpacking libglib2.0-0:armhf (2.40.0-3) ...
Selecting previously unselected package libcroco3:armhf.
Preparing to unpack .../libcroco3_0.6.8-2_armhf.deb ...
Unpacking libcroco3:armhf (0.6.8-2) ...
Selecting previously unselected package libunistring0:armhf.
Preparing to unpack .../libunistring0_0.9.3-5_armhf.deb ...
Unpacking libunistring0:armhf (0.9.3-5) ...
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Unpacking file (1:5.18-1) ...
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Unpacking gettext-base (0.18.3.2-1) ...
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Unpacking gettext (0.18.3.2-1) ...
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Preparing to unpack .../intltool-debian_0.35.0+20060710.1_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.1) ...
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Unpacking po-debconf (1.0.16+nmu2) ...
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Unpacking debhelper (9.20140228) ...
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Unpacking help2man (1.45.1) ...
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Preparing to unpack .../zlib1g-dev_1%3a1.2.8.dfsg-1_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Selecting previously unselected package sbuild-build-depends-discosnp-dummy.
Preparing to unpack .../sbuild-build-depends-discosnp-dummy.deb ...
Unpacking sbuild-build-depends-discosnp-dummy (0.invalid.0) ...
Processing triggers for install-info (5.2.0.dfsg.1-3) ...
Setting up libpipeline1:armhf (1.3.0-1) ...
Setting up groff-base (1.22.2-5) ...
Setting up bsdmainutils (9.0.5) ...
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 man-db (2.6.7.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasprintf0c2:armhf (0.18.3.2-1) ...
Setting up libmagic1:armhf (1:5.18-1) ...
Setting up libxml2:armhf (2.9.1+dfsg1-3) ...
Setting up libffi6:armhf (3.1~rc1+r3.0.13-12) ...
Setting up libglib2.0-0:armhf (2.40.0-3) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.8-2) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up bc (1.06.95-8) ...
Setting up file (1:5.18-1) ...
Setting up gettext-base (0.18.3.2-1) ...
Setting up gettext (0.18.3.2-1) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20140228) ...
Setting up help2man (1.45.1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-1) ...
Setting up sbuild-build-depends-discosnp-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.18-5) ...

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build environment                                                            │
└──────────────────────────────────────────────────────────────────────────────┘

Kernel: Linux 3.14-1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.24.51.20140425-1 dpkg-dev_1.17.6+rpi1 g++-4.8_4.8.2-21 gcc-4.8_4.8.2-21 libc6-dev_2.18-5 libstdc++-4.8-dev_4.8.2-21 libstdc++6_4.9.0-1 linux-libc-dev_3.13.10-1+rpi1
Package versions: apt_1.0.1 base-files_7.2+rpi1 base-passwd_3.5.28 bash_4.3-7 bc_1.06.95-8 binutils_2.24.51.20140425-1 bsdmainutils_9.0.5 bsdutils_1:2.20.1-5.7 build-essential_11.6 bzip2_1.0.6-5 coreutils_8.21-1.2 cpio_2.11+dfsg-2 cpp_4:4.8.2-3 cpp-4.8_4.8.2-21 dash_0.5.7-4 debconf_1.5.53 debconf-i18n_1.5.53 debfoster_2.7-1.2 debhelper_9.20140228 debianutils_4.4 diffutils_1:3.3-1 dpkg_1.17.6+rpi1 dpkg-dev_1.17.6+rpi1 e2fslibs_1.42.9-3 e2fsprogs_1.42.9-3 fakeroot_1.18.4-2 file_1:5.18-1 findutils_4.4.2-8 g++_4:4.8.2-3 g++-4.8_4.8.2-21 gcc_4:4.8.2-3 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8_4.8.2-21 gcc-4.8-base_4.8.2-21 gcc-4.9-base_4.9.0-1 gettext_0.18.3.2-1 gettext-base_0.18.3.2-1 gnupg_1.4.16-1.1 gpgv_1.4.16-1.1 grep_2.18-2 groff-base_1.22.2-5 gzip_1.6-3 help2man_1.45.1 hostname_3.15 init-system-helpers_1.18 initramfs-tools_0.115 initscripts_2.88dsf-53 insserv_1.14.0-5 install-info_5.2.0.dfsg.1-3 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.2-1+rpi1 kmod_16-2 libacl1_2.2.52-1 libapt-pkg4.12_1.0.1 libasan0_4.8.2-21 libasprintf0c2_0.18.3.2-1 libatomic1_4.9.0-1 libattr1_1:2.4.47-1 libaudit-common_1:2.3.6-1 libaudit1_1:2.3.6-1 libblkid1_2.20.1-5.7 libbz2-1.0_1.0.6-5 libc-bin_2.18-5 libc-dev-bin_2.18-5 libc6_2.18-5 libc6-dev_2.18-5 libcap2_1:2.22-1.2 libcloog-isl4_0.18.2-1 libcomerr2_1.42.9-3 libcroco3_0.6.8-2 libdb5.1_5.1.29-6 libdb5.3_5.3.28-3 libdbus-1-3_1.8.0-3 libdpkg-perl_1.17.6+rpi1 libffi6_3.1~rc1+r3.0.13-12 libgc1c2_1:7.2d-6 libgcc-4.8-dev_4.8.2-21 libgcc1_1:4.9.0-1 libgdbm3_1.8.3-12 libglib2.0-0_2.40.0-3 libgmp10_2:6.0.0+dfsg-2 libgomp1_4.9.0-1 libisl10_0.12.2-1 libklibc_2.0.2-1+rpi1 libkmod2_16-2 liblocale-gettext-perl_1.05-8 liblzma5_5.1.1alpha+20120614-2 libmagic1_1:5.18-1 libmount1_2.20.1-5.7 libmpc3_1.0.1-1 libmpfr4_3.1.2-1 libncurses5_5.9+20140118-1 libncursesw5_5.9+20140118-1 libpam-modules_1.1.8-3 libpam-modules-bin_1.1.8-3 libpam-runtime_1.1.8-3 libpam0g_1.1.8-3 libpcre3_1:8.31-5 libpipeline1_1.3.0-1 libprocps0_1:3.3.4-2 libprocps3_1:3.3.9-2 libreadline6_6.3-6 libselinux1_2.2.2-1 libsemanage-common_2.2-1 libsemanage1_2.2-1 libsepol1_2.2-1 libslang2_2.2.4-16 libss2_1.42.9-3 libstdc++-4.8-dev_4.8.2-21 libstdc++6_4.9.0-1 libtext-charwidth-perl_0.04-7+b3 libtext-iconv-perl_1.7-5+b3 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_2.3000-2 libtinfo5_5.9+20140118-1 libudev1_204-8 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-23.3 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.7 libxml2_2.9.1+dfsg1-3 linux-libc-dev_3.13.10-1+rpi1 login_1:4.1.5.1-1.1 lsb-base_4.1+Debian12+rpi1 make_3.81-8.3 makedev_2.3.1-93 man-db_2.6.7.1-1 mawk_1.3.3-17 mount_2.20.1-5.7 multiarch-support_2.18-5 nano_2.2.6-1.1 ncurses-base_5.9+20140118-1 ncurses-bin_5.9+20140118-1 passwd_1:4.1.5.1-1.1 patch_2.7.1-5 perl_5.18.2-2+b1 perl-base_5.18.2-2+b1 perl-modules_5.18.2-2 plymouth_0.8.8-16 po-debconf_1.0.16+nmu2 procps_1:3.3.9-2 raspbian-archive-keyring_20120528.2 readline-common_6.3-6 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-discosnp-dummy_0.invalid.0 sed_4.2.2-4 sensible-utils_0.0.9 startpar_0.59-3 sysv-rc_2.88dsf-53 sysvinit_2.88dsf-53 sysvinit-core_2.88dsf-53 sysvinit-utils_2.88dsf-53 tar_1.27.1-2 tzdata_2014b-1 udev_204-8 util-linux_2.20.1-5.7 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.8.dfsg-1 zlib1g-dev_1:1.2.8.dfsg-1

┌──────────────────────────────────────────────────────────────────────────────┐
│ Build                                                                        │
└──────────────────────────────────────────────────────────────────────────────┘


Unpack source
─────────────

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Thu May 29 13:03:30 2014 UTC using RSA key ID 326D8438
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./discosnp_1.2.2-1.dsc
dpkg-source: info: extracting discosnp in discosnp-1.2.2
dpkg-source: info: unpacking discosnp_1.2.2.orig.tar.gz
dpkg-source: info: unpacking discosnp_1.2.2-1.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
COLUMNS=80
CONSOLE=/dev/console
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INIT_VERSION=sysvinit-2.88
LC_ALL=POSIX
LINES=24
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PREVLEVEL=N
PWD=/
RUNLEVEL=2
SCHROOT_ALIAS_NAME=jessie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=jessie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=jessie-staging-armhf-sbuild-20bf2ba7-0f99-47a8-9a85-88bc439310b7
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
init=/sbin/init
previous=N
rootmnt=/root
runlevel=2

dpkg-buildpackage
─────────────────

dpkg-buildpackage: source package discosnp
dpkg-buildpackage: source version 1.2.2-1
dpkg-buildpackage: source distribution unstable
 dpkg-source --before-build discosnp-1.2.2
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
dh clean
   dh_testdir
   dh_auto_clean
   debian/rules override_dh_clean
make[1]: Entering directory `/«PKGBUILDDIR»'
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
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
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
dh build-arch
   dh_testdir -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o ../minia/Bank.o -c ../minia/Bank.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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:279:44: 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:710:44: 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:795:44: 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:985:65: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Bloom.cpp: In member function 'void Bloom::load(char*)':
../minia/Bloom.cpp:257:56: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o ../minia/Terminator.o -c ../minia/Terminator.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Terminator.cpp: In constructor 'BranchingTerminator::BranchingTerminator(BinaryBank*, uint64_t, Bloom*, Set*)':
../minia/Terminator.cpp:311:151: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=]
     fprintf (stderr,"\n\nAllocated memory for marking: %lld branching kmers x (%lu+%lu) B \n",nb_branching_kmers,sizeof(kmer_type),sizeof(set_value_t));
                                                                                                                                                       ^
../minia/Terminator.cpp:311:151: warning: format '%lu' expects argument of type 'long unsigned int', but argument 5 has type 'unsigned int' [-Wformat=]
../minia/Terminator.cpp:312:264: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'unsigned int' [-Wformat=]
     fprintf (stderr," actual implementation:  (sizeof(kmer_type) = %lu B) + (sizeof(set_value_t) = %lu B) per entry:  %.2f bits / solid kmer\n",sizeof(kmer_type),sizeof(set_value_t),(nb_branching_kmers*((sizeof(kmer_type)+sizeof(set_value_t))*8.0))/nb_solid_kmers);
                                                                                                                                                                                                                                                                        ^
../minia/Terminator.cpp:312:264: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'unsigned int' [-Wformat=]
../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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o ../minia/Traversal.o -c ../minia/Traversal.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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::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::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::basic_string<char> >::size_type {aka unsigned int}' [-Wformat=]
     if (debug) printf("%lu-bubble mean %d, stdev %.1f\n",consensuses.size(),mean,stdev);
                                                                                       ^
g++ -o ../minia/LinearCounter.o -c ../minia/LinearCounter.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o ../minia/Set.o -c ../minia/Set.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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: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:296:55: 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:297:110: 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:297:110: 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:300:12: 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:300:12: warning: format '%li' expects argument of type 'long int', but argument 3 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:300:12: 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:300:12: warning: format '%li' expects argument of type 'long int', but argument 5 has type 'unsigned int' [-Wformat=]
../minia/Set.cpp:300:12: 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:288:82: 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);
                                                                                  ^
g++ -o ../minia/Utils.o -c ../minia/Utils.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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:187:42: 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:199:54: 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:225:45: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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:56:50: 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:283:52: 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:537:56: 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");
                                                        ^
g++ -o ../minia/Debloom.o -c ../minia/Debloom.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
../minia/Debloom.cpp: In function 'void end_debloom_partition(bool)':
../minia/Debloom.cpp:29:39: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o Kmer_for_kissnp2.o -c Kmer_for_kissnp2.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o SNP.o -c SNP.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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:880:49: 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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
g++ -o IterativeExtensions.o -c IterativeExtensions.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER
IterativeExtensions.cpp: In static member function 'static void IterativeExtensions::construct_linear_seqs(std::string, std::string, int, std::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);
                                                                                                                              ^
g++ -o commons.o -c commons.cpp -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -O4 -lz -DMINIA_IS_IN_PARENT_FOLDER -Wl,-z,relro
kissnp2.cpp:70:1: warning: this decimal constant is unsigned only in ISO C90 [enabled by default]
 int64_t genome_size = 3000000000;
 ^
kissnp2.cpp: In function 'int main(int, char**)':
kissnp2.cpp:117:62: warning: too many arguments for format [-Wformat-extra-args]
     printf("This is kissnp2, version 2.1.1.5\n", getVersion());
                                                              ^
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 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
gcc  -o src/commons.o -c src/commons.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
src/commons.c: In function 'print_rev_comp':
src/commons.c:119:2: warning: passing argument 1 of 'fprintf' from incompatible pointer type [enabled by default]
  for(i=len-1;i>-1;i--)fprintf(out, "%c",comp[(int)s[i]]);
  ^
In file included from /usr/include/stdio.h:937:0,
                 from ./include/commons.h:47,
                 from src/commons.c:43:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:95:1: note: expected 'struct FILE * __restrict__' but argument is of type 'gzFile'
 fprintf (FILE *__restrict __stream, const char *__restrict __fmt, ...)
 ^
gcc  -o src/couple.o -c src/couple.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
gcc  -o src/extension_algorithm.o -c src/extension_algorithm.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
src/extension_algorithm.c: In function 'read_coherence':
src/extension_algorithm.c:349:4: warning: passing argument 1 of 'get_next_sequence_for_fastq' from incompatible pointer type [enabled by default]
    read_len = get_next_sequence_for_fastq(reads_file, read, quality,line);
    ^
In file included from src/extension_algorithm.c:47:0:
./include/commons.h:85:5: note: expected 'gzFile' but argument is of type 'struct FILE *'
 int get_next_sequence_for_fastq (gzFile file, char * read, char * quality, char * line);
     ^
src/extension_algorithm.c:351:4: warning: passing argument 1 of 'get_next_fasta_sequence' from incompatible pointer type [enabled by default]
    read_len = get_next_fasta_sequence(reads_file, read,line);
    ^
In file included from src/extension_algorithm.c:47:0:
./include/commons.h:83:5: note: expected 'gzFile' but argument is of type 'struct FILE *'
 int get_next_fasta_sequence (gzFile file, char * read, char * line);
     ^
gcc  -o src/fragment_index.o -c src/fragment_index.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
gcc  -o src/kissReads.o -c src/kissReads.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
src/kissReads.c: In function 'main':
src/kissReads.c:367:19: warning: assignment makes pointer from integer without a cast [enabled by default]
             found = strstr(reads_file_names[i],"fastq") || strstr(reads_file_names[i],"fq") || strstr(reads_file_names[i],"txt");
                   ^
src/kissReads.c:372:19: warning: assignment makes pointer from integer without a cast [enabled by default]
             found = strstr(reads_file_names[i],"fastq") || strstr(reads_file_names[i],"fq") || strstr(reads_file_names[i],"txt") || strstr(reads_file_names[i],"fa") || strstr(reads_file_names[i],"fasta") || strstr(reads_file_names[i],"fna");
                   ^
src/kissReads.c:436:9: warning: passing argument 1 of 'read_coherence' from incompatible pointer type [enabled by default]
         read_coherence(reads_files[i], reads_file_names[i], size_seeds,  min_coverage, results_against_set,  number_of_starters, i, quality, nb_events_per_set,  number_paths_per_event, sam_out, max_substitutions, no_subsutitution_on_central_position);
         ^
In file included from src/kissReads.c:46:0:
./include/extension_algorithm.h:52:7: note: expected 'struct FILE *' but argument is of type 'gzFile'
 float read_coherence (FILE * reads_file,
       ^
gcc  -o src/list.o -c src/list.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
gcc  -o src/outputs.o -c src/outputs.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
src/outputs.c: In function 'print_quadruplet_i':
src/outputs.c:535:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'double' [-Wformat=]
         fprintf(out, ">%s|", rank, results_against_set[cycle_id+1]->comment);
         ^
src/outputs.c:535:9: warning: too many arguments for format [-Wformat-extra-args]
src/outputs.c:543:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'double' [-Wformat=]
         fprintf(out, ">%s|", rank, results_against_set[cycle_id+2]->comment);
         ^
src/outputs.c:543:9: warning: too many arguments for format [-Wformat-extra-args]
src/outputs.c:551:9: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'double' [-Wformat=]
         fprintf(out, ">%s|", rank, results_against_set[cycle_id+3]->comment);
         ^
src/outputs.c:551:9: warning: too many arguments for format [-Wformat-extra-args]
gcc  -o src/interface_libchash.o -c src/interface_libchash.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
src/interface_libchash.c: In function 'hash_clear':
src/interface_libchash.c:136:16: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
   specific_free(data);
                ^
src/interface_libchash.c: In function 'hash_delete':
src/interface_libchash.c:170:16: warning: 'data' may be used uninitialized in this function [-Wmaybe-uninitialized]
   specific_free(data);
                ^
gcc  -o src/libchash.o -c src/libchash.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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' [-Wparentheses]
    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' [-Wparentheses]
    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 'HashFind':
src/libchash.c:1221:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
    LOAD_AND_RETURN(ht, Find(ht, KEY_TRUNC(ht, key), NULL));
    ^
src/libchash.c:1221:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
src/libchash.c: In function 'HashFindOrInsert':
src/libchash.c:1244:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
    return Insert(ht, KEY_TRUNC(ht, key), dataInsert, 0);
    ^
src/libchash.c: In function 'HashInsert':
src/libchash.c:1254:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
    return Insert(ht, KEY_TRUNC(ht, key), data, SAMEKEY_OVERWRITE);
    ^
src/libchash.c: In function 'HashDelete':
src/libchash.c:1264:4: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
    return Delete(ht, KEY_TRUNC(ht, key), !FAST_DELETE, 0);
    ^
src/libchash.c: In function 'HashFirstBucket':
src/libchash.c:1289:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
       if ( !IS_BCK_DELETED(retval) )
          ^
src/libchash.c: In function 'HashNextBucket':
src/libchash.c:1299:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
       if ( !IS_BCK_DELETED(retval) )
          ^
src/libchash.c: In function 'HashDoLoad':
src/libchash.c:1431:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
       if ( dataRead != NULL )        /* if it's null, we're done */
          ^
src/libchash.c: At top level:
src/libchash.c:691:18: warning: 'DenseFree' defined but not used [-Wunused-function]
 static DenseBin *DenseFree(DenseBin *bin, ulong cBuckets)
                  ^
src/libchash.c:710:21: warning: 'DenseInsert' defined but not used [-Wunused-function]
 static DenseBucket *DenseInsert(DenseBin *bin, DenseBucket *bckInsert,
                     ^
src/libchash.c:739:21: warning: 'DenseFirstBucket' defined but not used [-Wunused-function]
 static DenseBucket *DenseFirstBucket(DenseIterator *iter,
                     ^
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:767:14: warning: 'DenseRead' defined but not used [-Wunused-function]
 static ulong DenseRead(FILE *fp, DenseBin **pbin)
              ^
src/libchash.c:789:14: warning: 'DenseMemory' defined but not used [-Wunused-function]
 static ulong DenseMemory(ulong cBuckets, ulong cOccupied)
              ^
src/libchash.c: In function 'HashFind':
src/libchash.c:193:12: 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:193:12: 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:193:12: 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:193:12: 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:1407:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
    fread(szMagicKey, 1, 4, fp);
         ^
src/libchash.c:193:12: 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:193:12: 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:193:12: 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:193:12: 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:1423:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
    fread(rgchKeys, 1, cchKey, fp);
         ^
src/libchash.c:193:12: 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:193:12: 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:193:12: 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]);
   ^
gcc  -o src/tree.o -c src/tree.c -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -Wall -O3 -lz  -I./include/
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 src/tree.o  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -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
 fakeroot debian/rules binary-arch
debian/rules:39: warning: overriding commands for target `get-orig-source'
debian/rules:12: warning: ignoring old commands for target `get-orig-source'
dh binary-arch
   dh_testroot -a
   dh_prep -a
   dh_auto_install -a
   debian/rules override_dh_install
debian/rules:39: warning: overriding commands for target `get-orig-source'make[1]: Entering directory `/«PKGBUILDDIR»'

debian/rules:12: warning: ignoring old commands for target `get-orig-source'
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=1.2.2 kissnp2/kissnp2  > kissnp2.1
help2man --help-option=-h --no-discard-stderr --version-string=1.2.2 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_compress -a
   dh_fixperms -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
   dh_installdeb -a
   dh_gencontrol -a
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which is not NFS-safe
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package `discosnp' in `../discosnp_1.2.2-1_armhf.deb'.
 dpkg-genchanges -B -mRaspbian wandboard test autobuilder <root@raspbian.org> >../discosnp_1.2.2-1_armhf.changes
dpkg-genchanges: arch-specific upload - not including arch-independent packages
dpkg-genchanges: binary-only upload - not including any source code
 dpkg-source --after-build discosnp-1.2.2
dpkg-buildpackage: binary-only upload (no source included)
────────────────────────────────────────────────────────────────────────────────
Build finished at 20140604-0532

Finished
────────

I: Built successfully

┌──────────────────────────────────────────────────────────────────────────────┐
│ Changes                                                                      │
└──────────────────────────────────────────────────────────────────────────────┘


discosnp_1.2.2-1_armhf.changes:
───────────────────────────────

Format: 1.8
Date: Thu, 29 May 2014 14:09:41 +0200
Source: discosnp
Binary: discosnp
Architecture: armhf
Version: 1.2.2-1
Distribution: jessie-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Olivier Sallou <osallou@debian.org>
Description: 
 discosnp   - discovering Single Nucleotide Polymorphism from raw set(s) of rea
Changes: 
 discosnp (1.2.2-1) unstable; urgency=medium
 .
   * New upstream release
Checksums-Sha1: 
 635bf7a27c3ebd5a96bb7b8d1368d0784eef4013 125586 discosnp_1.2.2-1_armhf.deb
Checksums-Sha256: 
 2e1e0efb60d4271edec456946a9744ce47a19231f21cf9390a455e2e49303094 125586 discosnp_1.2.2-1_armhf.deb
Files: 
 b0d2c4405e310cfdccf3001078616215 125586 science optional discosnp_1.2.2-1_armhf.deb

┌──────────────────────────────────────────────────────────────────────────────┐
│ Package contents                                                             │
└──────────────────────────────────────────────────────────────────────────────┘


discosnp_1.2.2-1_armhf.deb
──────────────────────────

 new debian package, version 2.0.
 size 125586 bytes: control archive=1242 bytes.
    1048 bytes,    23 lines      control              
     850 bytes,    12 lines      md5sums              
 Package: discosnp
 Version: 1.2.2-1
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 264
 Depends: libc6 (>= 2.4), libgcc1 (>= 1:4.4.0), libstdc++6 (>= 4.3.0), 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.

drwxr-xr-x root/root         0 2014-06-04 05:32 ./
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/bin/
-rwxr-xr-x root/root      1612 2014-06-04 05:32 ./usr/bin/discoSnp_to_csv
-rwxr-xr-x root/root      2099 2014-06-04 05:32 ./usr/bin/discoSnp_to_genotypes
-rwxr-xr-x root/root    149456 2014-06-04 05:32 ./usr/bin/kissnp2
-rwxr-xr-x root/root     54864 2014-06-04 05:32 ./usr/bin/kissreads
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/share/
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/share/doc/
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/share/doc/discosnp/
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/share/doc/discosnp/examples/
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/share/doc/discosnp/examples/data_sample/
-rw-r--r-- root/root     13449 2013-10-14 18:51 ./usr/share/doc/discosnp/examples/data_sample/reads_sequence2.fasta.gz
-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       300 2014-05-29 12:08 ./usr/share/doc/discosnp/README.Debian
-rw-r--r-- root/root     26823 2014-05-29 12:08 ./usr/share/doc/discosnp/copyright
-rw-r--r-- root/root      4810 2014-05-20 07:44 ./usr/share/doc/discosnp/README.txt.gz
-rw-r--r-- root/root       314 2014-05-29 13:03 ./usr/share/doc/discosnp/changelog.Debian.gz
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/share/man/
drwxr-xr-x root/root         0 2014-06-04 05:32 ./usr/share/man/man1/
-rw-r--r-- root/root      1279 2014-06-04 05:32 ./usr/share/man/man1/kissnp2.1.gz
-rw-r--r-- root/root      1409 2014-06-04 05:32 ./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: 6056
Build-Time: 176
Distribution: jessie-staging
Host Architecture: armhf
Install-Time: 131
Job: discosnp_1.2.2-1
Machine Architecture: armhf
Package: discosnp
Package-Time: 356
Source-Version: 1.2.2-1
Space: 6056
Status: successful
Version: 1.2.2-1
────────────────────────────────────────────────────────────────────────────────
Finished at 20140604-0532
Build needed 00:05:56, 6056k disc space