Raspbian Package Auto-Building

Build log for bowtie2 (2.0.0-beta6-3) on armhf

bowtie22.0.0-beta6-3armhf → 2017-06-18 16:18:56

sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01

+==============================================================================+
| bowtie2 2.0.0-beta6-3 (armhf)                Sun, 18 Jun 2017 14:11:46 +0000 |
+==============================================================================+

Package: bowtie2
Version: 2.0.0-beta6-3
Source Version: 2.0.0-beta6-3
Distribution: wheezy-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf

I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/wheezy-staging-armhf-sbuild-ec52f773-bcab-461b-a5b1-4f031a69597d' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://172.17.0.1 wheezy-staging Release.gpg [473 B]
Get:2 http://172.17.0.1 wheezy-staging Release [10.8 kB]
Get:3 http://172.17.0.1 wheezy-staging/main Sources [6094 kB]
Get:4 http://172.17.0.1 wheezy-staging/main armhf Packages [7678 kB]
Fetched 13.8 MB in 6s (2014 kB/s)
Reading package lists...

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
Building dependency tree...
NOTICE: 'bowtie2' packaging is maintained in the 'Git' version control system at:
git://git.debian.org/debian-med/bowtie2.git
Need to get 5467 kB of source archives.
Get:1 http://172.17.0.1/private/ wheezy-staging/main bowtie2 2.0.0-beta6-3 (dsc) [2089 B]
Get:2 http://172.17.0.1/private/ wheezy-staging/main bowtie2 2.0.0-beta6-3 (tar) [5460 kB]
Get:3 http://172.17.0.1/private/ wheezy-staging/main bowtie2 2.0.0-beta6-3 (diff) [4500 B]
Fetched 5467 kB in 0s (6030 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bowtie2-crQFV0/bowtie2-2.0.0-beta6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bowtie2-crQFV0' 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-x1RvNk/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: keyring `/<<BUILDDIR>>/resolver-x1RvNk/gpg/secring.gpg' created
gpg: keyring `/<<BUILDDIR>>/resolver-x1RvNk/gpg/pubring.gpg' created
gpg: /<<BUILDDIR>>/resolver-x1RvNk/gpg/trustdb.gpg: trustdb created
gpg: key F90AF620: 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  (RSA: 1)
gpg: key F90AF620: secret key imported
gpg: key F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: Total number processed: 1
gpg:              unchanged: 1
gpg:       secret keys read: 1
gpg:   secret keys imported: 1
Get:1 copy: ./ Release.gpg [316 B]
Get:2 copy: ./ Release [957 B]
Get:3 copy: ./ Sources [350 B]
Get:4 copy: ./ Packages [432 B]
Fetched 2055 B in 0s (58.2 kB/s)
Reading package lists...
Reading package lists...

Install core build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 704 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x1RvNk/apt_archive/ ./ sbuild-build-depends-core-dummy 0.invalid.0 [704 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 704 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 11350 files and directories currently installed.)
Unpacking sbuild-build-depends-core-dummy (from .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (armhf included in any all)

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper (>= 8.0), help2man
Filtered Build-Depends: debhelper (>= 8.0), help2man
dpkg-deb: building package `sbuild-build-depends-bowtie2-dummy' in `/<<BUILDDIR>>/resolver-x1RvNk/apt_archive/sbuild-build-depends-bowtie2-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-bowtie2-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
Get:1 copy: ./ Release.gpg [316 B]
Get:2 copy: ./ Release [963 B]
Get:3 copy: ./ Sources [494 B]
Get:4 copy: ./ Packages [573 B]
Fetched 2346 B in 0s (65.4 kB/s)
Reading package lists...
Reading package lists...

Install bowtie2 build dependencies (apt-based resolver)
-------------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following extra packages will be installed:
  bsdmainutils debhelper file gettext gettext-base groff-base help2man
  html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
  libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
  po-debconf
Suggested packages:
  wamerican wordlist whois vacation dh-make gettext-doc groff less www-browser
  libmail-box-perl
Recommended packages:
  curl wget lynx-cur autopoint libglib2.0-data shared-mime-info xml-core
  libmail-sendmail-perl
The following NEW packages will be installed:
  bsdmainutils debhelper file gettext gettext-base groff-base help2man
  html2text intltool-debian libasprintf0c2 libcroco3 libffi5 libgettextpo0
  libglib2.0-0 libmagic1 libpcre3 libpipeline1 libunistring0 libxml2 man-db
  po-debconf sbuild-build-depends-bowtie2-dummy
0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded.
Need to get 9227 kB of archives.
After this operation, 24.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-x1RvNk/apt_archive/ ./ sbuild-build-depends-bowtie2-dummy 0.invalid.0 [714 B]
Get:2 http://172.17.0.1/private/ wheezy-staging/main libpcre3 armhf 1:8.30-5 [242 kB]
Get:3 http://172.17.0.1/private/ wheezy-staging/main libpipeline1 armhf 1.2.1-1 [35.0 kB]
Get:4 http://172.17.0.1/private/ wheezy-staging/main libasprintf0c2 armhf 0.18.1.1-9 [26.4 kB]
Get:5 http://172.17.0.1/private/ wheezy-staging/main libmagic1 armhf 5.11-2+deb7u9 [201 kB]
Get:6 http://172.17.0.1/private/ wheezy-staging/main libxml2 armhf 2.8.0+dfsg1-7+wheezy7 [826 kB]
Get:7 http://172.17.0.1/private/ wheezy-staging/main libffi5 armhf 3.0.10-3+b3 [22.9 kB]
Get:8 http://172.17.0.1/private/ wheezy-staging/main libglib2.0-0 armhf 2.33.12+really2.32.4-5 [1689 kB]
Get:9 http://172.17.0.1/private/ wheezy-staging/main libcroco3 armhf 0.6.6-2+deb7u1 [119 kB]
Get:10 http://172.17.0.1/private/ wheezy-staging/main libunistring0 armhf 0.9.3-5 [408 kB]
Get:11 http://172.17.0.1/private/ wheezy-staging/main libgettextpo0 armhf 0.18.1.1-9 [130 kB]
Get:12 http://172.17.0.1/private/ wheezy-staging/main bsdmainutils armhf 9.0.3 [207 kB]
Get:13 http://172.17.0.1/private/ wheezy-staging/main groff-base armhf 1.21-9 [1071 kB]
Get:14 http://172.17.0.1/private/ wheezy-staging/main man-db armhf 2.6.2-1 [1027 kB]
Get:15 http://172.17.0.1/private/ wheezy-staging/main file armhf 5.11-2+deb7u9 [53.2 kB]
Get:16 http://172.17.0.1/private/ wheezy-staging/main gettext-base armhf 0.18.1.1-9 [138 kB]
Get:17 http://172.17.0.1/private/ wheezy-staging/main html2text armhf 1.3.2a-15 [98.5 kB]
Get:18 http://172.17.0.1/private/ wheezy-staging/main gettext armhf 0.18.1.1-9 [1879 kB]
Get:19 http://172.17.0.1/private/ wheezy-staging/main intltool-debian all 0.35.0+20060710.1 [29.8 kB]
Get:20 http://172.17.0.1/private/ wheezy-staging/main po-debconf all 1.0.16+nmu2 [223 kB]
Get:21 http://172.17.0.1/private/ wheezy-staging/main debhelper all 9.20120909 [705 kB]
Get:22 http://172.17.0.1/private/ wheezy-staging/main help2man armhf 1.40.10 [96.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 9227 kB in 2s (4076 kB/s)
Selecting previously unselected package libpcre3:armhf.
(Reading database ... 11350 files and directories currently installed.)
Unpacking libpcre3:armhf (from .../libpcre3_1%3a8.30-5_armhf.deb) ...
Selecting previously unselected package libpipeline1:armhf.
Unpacking libpipeline1:armhf (from .../libpipeline1_1.2.1-1_armhf.deb) ...
Selecting previously unselected package libasprintf0c2:armhf.
Unpacking libasprintf0c2:armhf (from .../libasprintf0c2_0.18.1.1-9_armhf.deb) ...
Selecting previously unselected package libmagic1:armhf.
Unpacking libmagic1:armhf (from .../libmagic1_5.11-2+deb7u9_armhf.deb) ...
Selecting previously unselected package libxml2:armhf.
Unpacking libxml2:armhf (from .../libxml2_2.8.0+dfsg1-7+wheezy7_armhf.deb) ...
Selecting previously unselected package libffi5:armhf.
Unpacking libffi5:armhf (from .../libffi5_3.0.10-3+b3_armhf.deb) ...
Selecting previously unselected package libglib2.0-0:armhf.
Unpacking libglib2.0-0:armhf (from .../libglib2.0-0_2.33.12+really2.32.4-5_armhf.deb) ...
Selecting previously unselected package libcroco3:armhf.
Unpacking libcroco3:armhf (from .../libcroco3_0.6.6-2+deb7u1_armhf.deb) ...
Selecting previously unselected package libunistring0:armhf.
Unpacking libunistring0:armhf (from .../libunistring0_0.9.3-5_armhf.deb) ...
Selecting previously unselected package libgettextpo0:armhf.
Unpacking libgettextpo0:armhf (from .../libgettextpo0_0.18.1.1-9_armhf.deb) ...
Selecting previously unselected package bsdmainutils.
Unpacking bsdmainutils (from .../bsdmainutils_9.0.3_armhf.deb) ...
Selecting previously unselected package groff-base.
Unpacking groff-base (from .../groff-base_1.21-9_armhf.deb) ...
Selecting previously unselected package man-db.
Unpacking man-db (from .../man-db_2.6.2-1_armhf.deb) ...
Selecting previously unselected package file.
Unpacking file (from .../file_5.11-2+deb7u9_armhf.deb) ...
Selecting previously unselected package gettext-base.
Unpacking gettext-base (from .../gettext-base_0.18.1.1-9_armhf.deb) ...
Selecting previously unselected package html2text.
Unpacking html2text (from .../html2text_1.3.2a-15_armhf.deb) ...
Selecting previously unselected package gettext.
Unpacking gettext (from .../gettext_0.18.1.1-9_armhf.deb) ...
Selecting previously unselected package intltool-debian.
Unpacking intltool-debian (from .../intltool-debian_0.35.0+20060710.1_all.deb) ...
Selecting previously unselected package po-debconf.
Unpacking po-debconf (from .../po-debconf_1.0.16+nmu2_all.deb) ...
Selecting previously unselected package debhelper.
Unpacking debhelper (from .../debhelper_9.20120909_all.deb) ...
Selecting previously unselected package help2man.
Unpacking help2man (from .../help2man_1.40.10_armhf.deb) ...
Selecting previously unselected package sbuild-build-depends-bowtie2-dummy.
Unpacking sbuild-build-depends-bowtie2-dummy (from .../sbuild-build-depends-bowtie2-dummy_0.invalid.0_armhf.deb) ...
Setting up libpcre3:armhf (1:8.30-5) ...
Setting up libpipeline1:armhf (1.2.1-1) ...
Setting up libasprintf0c2:armhf (0.18.1.1-9) ...
Setting up libmagic1:armhf (5.11-2+deb7u9) ...
Setting up libxml2:armhf (2.8.0+dfsg1-7+wheezy7) ...
Setting up libffi5:armhf (3.0.10-3+b3) ...
Setting up libglib2.0-0:armhf (2.33.12+really2.32.4-5) ...
No schema files found: doing nothing.
Setting up libcroco3:armhf (0.6.6-2+deb7u1) ...
Setting up libunistring0:armhf (0.9.3-5) ...
Setting up libgettextpo0:armhf (0.18.1.1-9) ...
Setting up bsdmainutils (9.0.3) ...
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 groff-base (1.21-9) ...
Setting up man-db (2.6.2-1) ...
Building database of manual pages ...
Setting up file (5.11-2+deb7u9) ...
Setting up gettext-base (0.18.1.1-9) ...
Setting up html2text (1.3.2a-15) ...
Setting up gettext (0.18.1.1-9) ...
Setting up intltool-debian (0.35.0+20060710.1) ...
Setting up po-debconf (1.0.16+nmu2) ...
Setting up debhelper (9.20120909) ...
Setting up help2man (1.40.10) ...
Setting up sbuild-build-depends-bowtie2-dummy (0.invalid.0) ...

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 4.4.0-79-generic armhf (armv8l)
Toolchain package versions: binutils_2.22-8+deb7u3 dpkg-dev_1.16.18+rpi1 g++-4.6_4.6.3-14+rpi1 gcc-4.6_4.6.3-14+rpi1 libc6-dev_2.13-38+rpi2+deb7u11 libstdc++6_4.7.2-5+rpi1 libstdc++6-4.6-dev_4.6.3-14+rpi1 linux-libc-dev_3.2.51-1+rpi1
Package versions: apt_0.9.7.9+rpi1+deb7u7 base-files_7.1wheezy11+rpi1 base-passwd_3.5.26 bash_4.2+dfsg-0.1+deb7u4 binutils_2.22-8+deb7u3 bsdmainutils_9.0.3 bsdutils_1:2.20.1-5.3 build-essential_11.5+b1 bzip2_1.0.6-4 coreutils_8.13-3.5 cpio_2.11+dfsg-0.1+deb7u2 cpp_4:4.6.3-8 cpp-4.6_4.6.3-14+rpi1 dash_0.5.7-3 debconf_1.5.49 debconf-i18n_1.5.49 debfoster_2.7-1.2 debhelper_9.20120909 debianutils_4.3.2 diffutils_1:3.2-6 dpkg_1.16.18+rpi1 dpkg-dev_1.16.18+rpi1 e2fslibs_1.42.5-1.1+deb7u1 e2fsprogs_1.42.5-1.1+deb7u1 fakeroot_1.18.4-2 file_5.11-2+deb7u9 findutils_4.4.2-4 g++_4:4.6.3-8 g++-4.6_4.6.3-14+rpi1 gcc_4:4.6.3-8 gcc-4.5-base_4.5.3-12+rpi1 gcc-4.6_4.6.3-14+rpi1 gcc-4.6-base_4.6.3-14+rpi1 gcc-4.7-base_4.7.2-5+rpi1 gettext_0.18.1.1-9 gettext-base_0.18.1.1-9 gnupg_1.4.12-7+deb7u8 gpgv_1.4.12-7+deb7u8 grep_2.12-2 groff-base_1.21-9 gzip_1.5-1.1 help2man_1.40.10 hostname_3.11 html2text_1.3.2a-15 initramfs-tools_0.115~bpo70+1 initscripts_2.88dsf-41+deb7u1 insserv_1.14.0-5 intltool-debian_0.35.0+20060710.1 klibc-utils_2.0.1-3.1+rpi1 kmod_9-3 libacl1_2.2.51-8 libapt-pkg4.12_0.9.7.9+rpi1+deb7u7 libasprintf0c2_0.18.1.1-9 libattr1_1:2.4.46-8 libblkid1_2.20.1-5.3 libbz2-1.0_1.0.6-4 libc-bin_2.13-38+rpi2+deb7u11 libc-dev-bin_2.13-38+rpi2+deb7u11 libc6_2.13-38+rpi2+deb7u11 libc6-dev_2.13-38+rpi2+deb7u11 libclass-isa-perl_0.36-3 libcomerr2_1.42.5-1.1+deb7u1 libcroco3_0.6.6-2+deb7u1 libdb5.1_5.1.29-5 libdbus-1-3_1.6.8-1+deb7u6 libdpkg-perl_1.16.18+rpi1 libffi5_3.0.10-3+b3 libgc1c2_1:7.1-9.1+deb7u1 libgcc1_1:4.7.2-5+rpi1 libgdbm3_1.8.3-11 libgettextpo0_0.18.1.1-9 libglib2.0-0_2.33.12+really2.32.4-5 libgmp10_2:5.0.5+dfsg-2 libgomp1_4.7.2-5+rpi1 libklibc_2.0.1-3.1+rpi1 libkmod2_9-3 liblocale-gettext-perl_1.05-7 liblzma5_5.1.1alpha+20120614-2 libmagic1_5.11-2+deb7u9 libmount1_2.20.1-5.3 libmpc2_0.9-4 libmpfr4_3.1.0-5 libncurses5_5.9-10 libncursesw5_5.9-10 libnih-dbus1_1.0.3-4.1 libnih1_1.0.3-4.1 libpam-modules_1.1.3-7.1 libpam-modules-bin_1.1.3-7.1 libpam-runtime_1.1.3-7.1 libpam0g_1.1.3-7.1 libpcre3_1:8.30-5 libpipeline1_1.2.1-1 libprocps0_1:3.3.3-3 libreadline6_6.2+dfsg-0.1 libselinux1_2.1.9-5 libsemanage-common_2.1.6-6 libsemanage1_2.1.6-6 libsepol1_2.1.4-3 libslang2_2.2.4-15 libss2_1.42.5-1.1+deb7u1 libstdc++6_4.7.2-5+rpi1 libstdc++6-4.6-dev_4.6.3-14+rpi1 libswitch-perl_2.16-2 libtext-charwidth-perl_0.04-7 libtext-iconv-perl_1.7-5 libtext-wrapi18n-perl_0.06-7 libtimedate-perl_1.2000-1 libtinfo5_5.9-10 libudev0_175-7.2 libunistring0_0.9.3-5 libusb-0.1-4_2:0.1.12-20+nmu1 libustr-1.0-1_1.0.4-3 libuuid1_2.20.1-5.3 libxml2_2.8.0+dfsg1-7+wheezy7 linux-libc-dev_3.2.51-1+rpi1 login_1:4.1.5.1-1+deb7u1 lsb-base_4.1+Debian8+rpi1+deb7u1 make_3.81-8.2 makedev_2.3.1-92 man-db_2.6.2-1 mawk_1.3.3-17 mount_2.20.1-5.3 mountall_2.46 multiarch-support_2.13-38+rpi2+deb7u11 ncurses-base_5.9-10 ncurses-bin_5.9-10 passwd_1:4.1.5.1-1+deb7u1 patch_2.6.1-3 perl_5.14.2-21+rpi2+deb7u2 perl-base_5.14.2-21+rpi2+deb7u2 perl-modules_5.14.2-21+rpi2+deb7u2 plymouth_0.8.5.1-5 po-debconf_1.0.16+nmu2 procps_1:3.3.3-3 raspbian-archive-keyring_20120528.2 readline-common_6.2+dfsg-0.1 sbuild-build-depends-bowtie2-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.2.1-10 sensible-utils_0.0.7 sysv-rc_2.88dsf-41+deb7u1 sysvinit_2.88dsf-41+deb7u1 sysvinit-utils_2.88dsf-41+deb7u1 tar_1.26+dfsg-0.1+deb7u1 tzdata_2017b-0+deb7u1 udev_175-7.2 util-linux_2.20.1-5.3 xz-utils_5.1.1alpha+20120614-2 zlib1g_1:1.2.7.dfsg-13

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

gpgv: keyblock resource `/sbuild-nonexistent/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Fri Jun  1 20:15:39 2012 UTC using RSA key ID 1B5228B0
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on ./bowtie2_2.0.0-beta6-3.dsc
dpkg-source: info: extracting bowtie2 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking bowtie2_2.0.0-beta6.orig.tar.gz
dpkg-source: info: unpacking bowtie2_2.0.0-beta6-3.debian.tar.gz
dpkg-source: info: applying bowtie2_gcc4.7.patch
dpkg-source: info: applying fix_makefile_machine_detection.patch

Check disk space
----------------

df: Warning: cannot read table of mounted file systems: No such file or directory
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=wheezy-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=wheezy-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=wheezy-staging-armhf-sbuild-ec52f773-bcab-461b-a5b1-4f031a69597d
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

dpkg-buildpackage
-----------------

dpkg-buildpackage: source package bowtie2
dpkg-buildpackage: source version 2.0.0-beta6-3
 dpkg-source --before-build bowtie2-2.0.0-beta6
dpkg-buildpackage: host architecture armhf
 fakeroot debian/rules clean
dh clean
   dh_testdir
   dh_auto_clean
make[1]: Entering directory `/<<PKGBUILDDIR>>'
rm -f bowtie2-build bowtie2-align bowtie2-inspect bowtie2-build-debug bowtie2-align-debug bowtie2-inspect-debug \
	bowtie2-build.exe bowtie2-align.exe bowtie2-inspect.exe bowtie2-build-debug.exe bowtie2-align-debug.exe bowtie2-inspect-debug.exe \
	bowtie2-src.zip bowtie2-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
make[1]: Leaving directory `/<<PKGBUILDDIR>>'
   dh_clean
 debian/rules build-arch
dh build-arch
   dh_testdir -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
make[1]: Entering directory `/<<PKGBUILDDIR>>'
dh_auto_build -- ENABLE_SSE=
make[2]: Entering directory `/<<PKGBUILDDIR>>'
/usr/bin/g++ -O3   -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 \""  \
		-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
		 \
		-o bowtie2-build bt2_build.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp diff_sample.cpp bowtie_build_main.cpp \
		 
ref_read.cpp: In function 'void reverseRefRecords(const EList<RefRecord>&, EList<RefRecord>&, bool, bool)':
ref_read.cpp:223:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<unsigned int, unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:283:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::printQAlign(std::ostream&, const char*, const BTDnaString&, const EList<Edit>&)':
edit.cpp:100:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:124:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:146:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::printQAlignNoCheck(std::ostream&, const char*, const BTDnaString&, const EList<Edit>&)':
edit.cpp:180:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:201:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:222:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::toRef(const BTDnaString&, const EList<Edit>&, BTDnaString&, bool, size_t, size_t)':
edit.cpp:277:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static bool Edit::repOk(const EList<Edit>&, const BTDnaString&, bool, size_t, size_t)':
edit.cpp:358:8: warning: variable 'del' set but not used [-Wunused-but-set-variable]
edit.cpp:358:21: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:358:34: warning: variable 'mm' set but not used [-Wunused-but-set-variable]
bt2_idx.cpp: In member function 'void Ebwt::countBt2SideRange(SideLocus&, uint32_t, uint32_t*, uint32_t*, EList<bool>*) const':
bt2_idx.cpp:903:7: warning: variable 'adjustedForDollar' set but not used [-Wunused-but-set-variable]
bt2_util.cpp: In member function 'void Ebwt::sanityCheckUpToSide(int) const':
bt2_util.cpp:42:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable]
reference.cpp: In static member function 'static std::pair<unsigned int, unsigned int> BitPairReference::szsFromFasta(EList<FileBuf*>&, const string&, bool, const RefReadInParams&, EList<RefRecord>&, bool)':
reference.cpp:612:30: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable]
/usr/bin/g++ -O3   -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 \""  \
		-fno-strict-aliasing -DBOWTIE2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_PTHREADS -DPREFETCH_LOCALITY=2 -DBOWTIE_MM  -DBOWTIE2 -DNDEBUG -Wall \
		 \
		-o bowtie2-align bt2_search.cpp \
		ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp bt2_io.cpp bt2_util.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp qual.cpp pat.cpp sam.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp bowtie_main.cpp \
		 -lpthread
In file included from bt2_search.cpp:47:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
ref_read.cpp: In function 'void reverseRefRecords(const EList<RefRecord>&, EList<RefRecord>&, bool, bool)':
ref_read.cpp:223:8: warning: variable 'mergedLast' set but not used [-Wunused-but-set-variable]
ref_read.cpp: In function 'std::pair<unsigned int, unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, int&)':
ref_read.cpp:283:18: warning: variable 'rpcp' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::printQAlign(std::ostream&, const char*, const BTDnaString&, const EList<Edit>&)':
edit.cpp:100:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:124:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:146:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::printQAlignNoCheck(std::ostream&, const char*, const BTDnaString&, const EList<Edit>&)':
edit.cpp:180:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:201:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:222:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static void Edit::toRef(const BTDnaString&, const EList<Edit>&, BTDnaString&, bool, size_t, size_t)':
edit.cpp:277:8: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp: In static member function 'static bool Edit::repOk(const EList<Edit>&, const BTDnaString&, bool, size_t, size_t)':
edit.cpp:358:8: warning: variable 'del' set but not used [-Wunused-but-set-variable]
edit.cpp:358:21: warning: variable 'ins' set but not used [-Wunused-but-set-variable]
edit.cpp:358:34: warning: variable 'mm' set but not used [-Wunused-but-set-variable]
bt2_idx.cpp: In member function 'void Ebwt::countBt2SideRange(SideLocus&, uint32_t, uint32_t*, uint32_t*, EList<bool>*) const':
bt2_idx.cpp:903:7: warning: variable 'adjustedForDollar' set but not used [-Wunused-but-set-variable]
bt2_util.cpp: In member function 'void Ebwt::sanityCheckUpToSide(int) const':
bt2_util.cpp:42:11: warning: variable 'occ_save' set but not used [-Wunused-but-set-variable]
reference.cpp: In static member function 'static std::pair<unsigned int, unsigned int> BitPairReference::szsFromFasta(EList<FileBuf*>&, const string&, bool, const RefReadInParams&, EList<RefRecord>&, bool)':
reference.cpp:612:30: warning: variable 'sztot2' set but not used [-Wunused-but-set-variable]
pat.cpp: In member function 'virtual bool FastaPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)':
pat.cpp:747:7: warning: variable 'warning' set but not used [-Wunused-but-set-variable]
read_qseq.cpp: In member function 'virtual bool QseqPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)':
read_qseq.cpp:250:7: warning: variable 'c' set but not used [-Wunused-but-set-variable]
In file included from aligner_sw.cpp:25:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_sw_driver.h:81:0,
                 from aligner_sw_driver.cpp:47:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
aligner_result.cpp: In member function 'bool AlnRes::overlap(AlnRes&)':
aligner_result.cpp:328:10: warning: variable 'fivep' set but not used [-Wunused-but-set-variable]
aligner_result.cpp: In member function 'void AlnRes::printCigar(bool, EList<char>&, EList<unsigned int>&, BTString*, char*) const':
aligner_result.cpp:648:8: warning: variable 'printed' set but not used [-Wunused-but-set-variable]
pe.cpp: In member function 'int PairedEndPolicy::peClassifyPair(int64_t, size_t, bool, int64_t, size_t, bool) const':
pe.cpp:129:7: warning: variable 'dovetailing' set but not used [-Wunused-but-set-variable]
aln_sink.cpp: In member function 'void AlnSinkWrap::finishRead(const SeedResults*, const SeedResults*, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, RandomSource&, ReportingMetrics&, const PerReadMetrics&, bool, bool)':
aln_sink.cpp:862:11: warning: variable 'off' set but not used [-Wunused-but-set-variable]
In file included from aligner_bt.h:31:0,
                 from aligner_bt.cpp:20:
sse_util.h:27:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from sse_util.cpp:20:0:
sse_util.h:27:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse.h:28:0,
                 from aligner_swsse.cpp:22:
sse_util.h:27:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse_loc_i16.cpp:56:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse_ee_i16.cpp:56:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse_loc_u8.cpp:56:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
In file included from aligner_swsse_ee_u8.cpp:56:0:
aligner_sw.h:72:23: fatal error: emmintrin.h: No such file or directory
compilation terminated.
make[2]: *** [bowtie2-align] Error 1
make[2]: Leaving directory `/<<PKGBUILDDIR>>'
dh_auto_build: make -j1 ENABLE_SSE= returned exit code 2
make[1]: *** [override_dh_auto_build] Error 2
make[1]: Leaving directory `/<<PKGBUILDDIR>>'
make: *** [build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch gave error exit status 2
--------------------------------------------------------------------------------
Build finished at 2017-06-18T14:16:00Z

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: armhf
Build-Space: 22792
Build-Time: 177
Distribution: wheezy-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 60
Job: bowtie2_2.0.0-beta6-3
Machine Architecture: armhf
Package: bowtie2
Package-Time: 254
Source-Version: 2.0.0-beta6-3
Space: 22792
Status: attempted
Version: 2.0.0-beta6-3
--------------------------------------------------------------------------------
Finished at 2017-06-18T14:16:00Z
Build needed 00:04:14, 22792k disk space