Build log for libstatgen (1.0.14-2) on armhf

libstatgen → 1.0.14-2 → armhf → 2018-10-11 01:11:15

sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04

+==============================================================================+
| libstatgen 1.0.14-2 (armhf)                  Wed, 10 Oct 2018 23:35:36 +0000 |
+==============================================================================+

Package: libstatgen
Version: 1.0.14-2
Source Version: 1.0.14-2
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-68178071-cda2-44c6-983e-753be2a7e166' with '<<CHROOT>>'

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

Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.1 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.8 MB]
Fetched 23.9 MB in 26s (914 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'libstatgen' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/libstatgen.git
Please use:
git clone https://salsa.debian.org/med-team/libstatgen.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 581 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main libstatgen 1.0.14-2 (dsc) [2155 B]
Get:2 http://172.17.0.1/private buster-staging/main libstatgen 1.0.14-2 (tar) [559 kB]
Get:3 http://172.17.0.1/private buster-staging/main libstatgen 1.0.14-2 (diff) [20.0 kB]
Fetched 581 kB in 0s (3970 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/libstatgen-vO2wmD/libstatgen-1.0.14' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libstatgen-vO2wmD' 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-xMTIDu/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-xMTIDu/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-xMTIDu/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-xMTIDu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (3118 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session libexpat1 libnss-systemd
  libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
  sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 79 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13941 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Arch check ok (armhf included in any all)

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


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

Merged Build-Depends: debhelper (>= 11), doxygen, libssl-dev, zlib1g-dev, d-shlibs
Filtered Build-Depends: debhelper (>= 11), doxygen, libssl-dev, zlib1g-dev, d-shlibs
dpkg-deb: building package 'sbuild-build-depends-libstatgen-dummy' in '/<<BUILDDIR>>/resolver-xMTIDu/apt_archive/sbuild-build-depends-libstatgen-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning:   sbuild-build-depends-core-dummy sbuild-build-depends-libstatgen-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-xMTIDu/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ Sources [514 B]
Get:5 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ Packages [596 B]
Fetched 2443 B in 1s (3592 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
  ca-certificates dbus dbus-user-session libexpat1 libnss-systemd
  libpam-systemd openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper
  dh-autoreconf dh-strip-nondeterminism doxygen dwz file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libbsd0 libclang1-6.0
  libcroco3 libedit2 libelf1 libfile-stripnondeterminism-perl libfreetype6
  libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 libllvm6.0
  libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libssl-dev libtool
  libxapian30 libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
  vacation dh-make doxygen-latex doxygen-doc doxygen-gui graphviz gettext-doc
  libasprintf-dev libgettextpo-dev groff libssl-doc libtool-doc gfortran
  | fortran95-compiler gcj-jdk xapian-tools m4-doc apparmor less www-browser
  libmail-box-perl
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
  xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdmainutils d-shlibs debhelper
  dh-autoreconf dh-strip-nondeterminism doxygen dwz file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libbsd0 libclang1-6.0
  libcroco3 libedit2 libelf1 libfile-stripnondeterminism-perl libfreetype6
  libglib2.0-0 libgraphite2-3 libharfbuzz0b libicu-le-hb0 libicu60 libllvm6.0
  libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libssl-dev libtool
  libxapian30 libxml2 m4 man-db po-debconf
  sbuild-build-depends-libstatgen-dummy zlib1g-dev
0 upgraded, 43 newly installed, 0 to remove and 79 not upgraded.
Need to get 42.7 MB/43.2 MB of archives.
After this operation, 164 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-xMTIDu/apt_archive ./ sbuild-build-depends-libstatgen-dummy 0.invalid.0 [888 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.4-2 [1161 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.34-2 [239 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.34-2 [107 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.34-2 [65.0 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-7 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf libedit2 armhf 3.1-20180525-1 [70.6 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-1.1 [771 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-7 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf d-shlibs all 0.82+nmu1 [19.2 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-4 [547 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.043-1 [20.2 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.043-1 [12.1 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.170-0.5 [160 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-2 [67.4 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.1-2 [1051 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libgraphite2-3 armhf 1.3.12-1 [69.1 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libharfbuzz0b armhf 1.9.0-1+rpi1 [877 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libicu-le-hb0 armhf 1.0.3+git161113-5 [12.8 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libicu60 armhf 60.2-6 [7789 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7 [602 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-7 [1218 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.4.1 [989 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libllvm6.0 armhf 1:6.0.1-9+rpi1 [12.5 MB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libclang1-6.0 armhf 1:6.0.1-9+rpi1 [5684 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libxapian30 armhf 1.4.7-4 [949 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf doxygen armhf 1.8.13-10 [3257 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libssl-dev armhf 1.1.0h-4 [1376 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Processing triggers for libc-bin (2.27-5+rpi1) ...
Setting up dwz (0.12-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up autopoint (0.19.8.1-7) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.043-1) ...
Setting up libedit2:armhf (3.1-20180525-1) ...
Setting up libllvm6.0:armhf (1:6.0.1-9+rpi1) ...
Setting up libclang1-6.0:armhf (1:6.0.1-9+rpi1) ...
Setting up libharfbuzz0b:armhf (1.9.0-1+rpi1) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.34-2) ...
Setting up automake (1:1.16.1-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtool (2.4.6-4) ...
Setting up doxygen (1.8.13-10) ...
Setting up dh-autoreconf (19) ...
Setting up libicu-le-hb0:armhf (1.0.3+git161113-5) ...
Setting up dh-strip-nondeterminism (0.043-1) ...
Setting up libicu60:armhf (60.2-6) ...
Setting up libxml2:armhf (2.9.4+dfsg1-7) ...
Setting up libcroco3:armhf (0.6.12-2) ...
Setting up gettext (0.19.8.1-7) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up po-debconf (1.0.20) ...
Setting up debhelper (11.4.1) ...
Setting up sbuild-build-depends-libstatgen-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges

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

Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-2+rpi1 dpkg-dev_1.19.0.5 g++-8_8.1.0-12+rpi1 gcc-8_8.1.0-12+rpi1 libc6-dev_2.27-5+rpi1 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 linux-libc-dev_4.16.16-2+rpi1
Package versions: adduser_3.117 apt_1.6.3 autoconf_2.69-11 automake_1:1.16.1-1.1 autopoint_0.19.8.1-7 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-3.1 binutils_2.31.1-2+rpi1 binutils-arm-linux-gnueabihf_2.31.1-2+rpi1 binutils-common_2.31.1-2+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.32.1-0.1 build-essential_12.5 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:8.1.0-1+rpi1 cpp-8_8.1.0-12+rpi1 d-shlibs_0.82+nmu1 dash_0.5.8-2.10 dbus_1.12.10-1 dbus-user-session_1.12.10-1 debconf_1.5.69 debhelper_11.4.1 debianutils_4.8.6 dh-autoreconf_19 dh-strip-nondeterminism_0.043-1 diffutils_1:3.6-1 dirmngr_2.2.9-1+rpi1 dmsetup_2:1.02.145-4.1+b4 doxygen_1.8.13-10 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 dwz_0.12-2 e2fslibs_1.44.3-1 e2fsprogs_1.44.3-1 fakeroot_1.23-1 fdisk_2.32.1-0.1 file_1:5.34-2 findutils_4.6.0+git+20171230-2 g++_4:8.1.0-1+rpi1 g++-8_8.1.0-12+rpi1 gcc_4:8.1.0-1+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.4.0-18+rpi1 gcc-8_8.1.0-12+rpi1 gcc-8-base_8.1.0-12+rpi1 gettext_0.19.8.1-7 gettext-base_0.19.8.1-7 gnupg_2.2.9-1+rpi1 gnupg-l10n_2.2.9-1+rpi1 gnupg-utils_2.2.9-1+rpi1 gpg_2.2.9-1+rpi1 gpg-agent_2.2.9-1+rpi1 gpg-wks-client_2.2.9-1+rpi1 gpg-wks-server_2.2.9-1+rpi1 gpgconf_2.2.9-1+rpi1 gpgsm_2.2.9-1+rpi1 gpgv_2.2.9-1+rpi1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.9-2 hostname_3.20 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-14+rpi1 kmod_25-1 libacl1_2.2.52-3 libapparmor1_2.13-8 libapt-pkg5.0_1.6.3 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.1.0-12+rpi1 libassuan0_2.5.1-2 libatomic1_8.1.0-12+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.3-1 libaudit1_1:2.8.3-1 libbinutils_2.31.1-2+rpi1 libblkid1_2.32.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-5+rpi1 libc-dev-bin_2.27-5+rpi1 libc6_2.27-5+rpi1 libc6-dev_2.27-5+rpi1 libcap-ng0_0.7.9-1 libcap2_1:2.25-1.2 libcc1-0_8.1.0-12+rpi1 libclang1-6.0_1:6.0.1-9+rpi1 libcom-err2_1.44.3-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.4-2 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.10-1 libdebconfclient0_0.244 libdevmapper1.02.1_2:1.02.145-4.1+b4 libdpkg-perl_1.19.0.5 libdrm-common_2.4.92-1+rpi1 libdrm2_2.4.92-1+rpi1 libedit2_3.1-20180525-1 libelf1_0.170-0.5 libexpat1_2.2.5-3 libext2fs2_1.44.3-1 libfakeroot_1.23-1 libfdisk1_2.32.1-0.1 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.043-1 libfreetype6_2.8.1-2 libgcc-8-dev_8.1.0-12+rpi1 libgcc1_1:8.1.0-12+rpi1 libgcrypt20_1.8.3-1 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libglib2.0-0_2.58.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.19-1 libgomp1_8.1.0-12+rpi1 libgpg-error0_1.32-1 libgraphite2-3_1.3.12-1 libharfbuzz0b_1.9.0-1+rpi1 libhogweed4_3.4-1 libicu-le-hb0_1.0.3+git161113-5 libicu60_60.2-6 libidn11_1.33-2.2 libidn2-0_2.0.4-2.2 libip4tc0_1.6.2-1.1 libisl19_0.20-1 libjson-c3_0.12.1-1.3 libklibc_2.0.4-14+rpi1 libkmod2_25-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.46+dfsg-5+rpi1 libldap-common_2.4.46+dfsg-5+rpi1 libllvm6.0_1:6.0.1-9+rpi1 liblocale-gettext-perl_1.07-3+b2 liblz4-1_1.8.2-1+rpi1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.34-2 libmagic1_1:5.34-2 libmount1_2.32.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1+20180714-1 libncurses6_6.1+20180714-1 libncursesw5_6.1+20180714-1 libncursesw6_6.1+20180714-1 libnettle6_3.4-1 libnpth0_1.6-1 libnss-systemd_239-7 libp11-kit0_0.23.12-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_239-7 libpam0g_1.1.8-3.7 libpcre3_2:8.39-10 libperl5.26_5.26.2-7 libpipeline1_1.5.0-1 libplymouth4_0.9.3-3 libpng16-16_1.6.34-2+rpi1 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-3 libselinux1_2.8-1 libsemanage-common_2.8-1 libsemanage1_2.8-1 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.32.1-0.1 libsqlite3-0_3.24.0-1 libss2_1.44.3-1 libssl-dev_1.1.0h-4 libssl1.1_1.1.0h-4 libstdc++-8-dev_8.1.0-12+rpi1 libstdc++6_8.1.0-12+rpi1 libsystemd0_239-7 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20180714-1 libtinfo6_6.1+20180714-1 libtool_2.4.6-4 libubsan1_8.1.0-12+rpi1 libudev1_239-7 libunistring2_0.9.10-1 libuuid1_2.32.1-0.1 libxapian30_1.4.7-4 libxml2_2.9.4+dfsg1-7 libzstd1_1.3.4+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.16.16-2+rpi1 login_1:4.5-1.1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.2.1-1.2 makedev_2.3.1-93 man-db_2.8.4-2 mawk_1.3.3-17 mount_2.32.1-0.1 multiarch-support_2.27-5+rpi1 nano_2.9.8-1 ncurses-base_6.1+20180714-1 ncurses-bin_6.1+20180714-1 netbase_5.4 openssl_1.1.0h-4 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.26.2-7 perl-base_5.26.2-7 perl-modules-5.26_5.26.2-7 pinentry-curses_1.1.0-1 plymouth_0.9.3-3 po-debconf_1.0.20 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libstatgen-dummy_0.invalid.0 sed_4.5-1 sensible-utils_0.0.12 systemd_239-7 systemd-sysv_239-7 sysvinit-utils_2.88dsf-59.10 tar_1.30+dfsg-2 tzdata_2018e-1 udev_239-7 util-linux_2.32.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1

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


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

gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Sep 20 19:21:38 2018 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libstatgen_1.0.14-2.dsc
dpkg-source: info: extracting libstatgen in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking libstatgen_1.0.14.orig.tar.gz
dpkg-source: info: unpacking libstatgen_1.0.14-2.debian.tar.xz
dpkg-source: info: applying Fix_compilation_error.patch
dpkg-source: info: applying Fix_compilation_flags.patch
dpkg-source: info: applying Remove_erroneous_deletes_in_Chromosome_constructor.patch

Check disc space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=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-68178071-cda2-44c6-983e-753be2a7e166
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd

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

dpkg-buildpackage: info: source package libstatgen
dpkg-buildpackage: info: source version 1.0.14-2
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build libstatgen-1.0.14
dpkg-buildpackage: info: host architecture armhf
 fakeroot debian/rules clean
dh clean
   dh_auto_clean
	make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>/samtools'
rm -f  ../include/bgzf.h ../include/knetfile.h ../include/khash.h ../include/bam.h
ar d ../libStatGen.a obj/bgzf.o obj/knetfile.o
ar: creating ../libStatGen.a
ranlib ../libStatGen.a
ar d ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o
ar: creating ../libStatGen_debug.a
ranlib ../libStatGen_debug.a
ar d ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o
ar: creating ../libStatGen_profile.a
ranlib ../libStatGen_profile.a
rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ 
make[2]: Leaving directory '/<<PKGBUILDDIR>>/samtools'
make[2]: Entering directory '/<<PKGBUILDDIR>>/general'
rm -f  ../include/BaseAsciiMap.h ../include/BaseQualityHelper.h ../include/BaseUtilities.h ../include/BasicHash.h ../include/BgzfFileType.h ../include/BgzfFileTypeRecovery.h ../include/CharBuffer.h ../include/Chromosome.h ../include/Cigar.h ../include/CigarRoller.h ../include/Error.h ../include/ErrorHandler.h ../include/FileType.h ../include/FortranFormat.h ../include/GenomeSequence.h ../include/GenotypeLists.h ../include/glfHandler.h ../include/GzipFileType.h ../include/GzipHeader.h ../include/Hash.h ../include/IndexBase.h ../include/Input.h ../include/InputFile.h ../include/IntArray.h ../include/IntHash.h ../include/LongLongCounter.h ../include/MapFunction.h ../include/MathMatrix.h ../include/MathVector.h ../include/MemoryAllocators.h ../include/MemoryInfo.h ../include/MemoryMapArray.h ../include/MemoryMap.h ../include/MiniDeflate.h ../include/NonOverlapRegions.h ../include/Parameters.h ../include/PedigreeAlleleFreq.h ../include/Pedigree.h ../include/PedigreeDescription.h ../include/PedigreeFamily.h ../include/PedigreeGlobals.h ../include/PedigreePerson.h ../include/PhoneHome.h ../include/QuickIndex.h ../include/Random.h ../include/ReferenceSequence.h ../include/SmithWaterman.h ../include/Sort.h ../include/STLUtilities.h ../include/StatGenStatus.h ../include/StringAlias.h ../include/StringArray.h ../include/StringBasics.h ../include/StringHash.h ../include/StringMap.h ../include/Tabix.h ../include/UncompressedFileType.h ../include/Constant.h ../include/CSG_MD5.h ../include/Generic.h ../include/GenomeSequenceHelpers.h ../include/GreedyTupleAligner.h ../include/InplaceMerge.h ../include/LongHash.h ../include/LongInt.h ../include/MathConstant.h ../include/PackedVector.h ../include/PedigreeAlleles.h ../include/Performance.h ../include/ReusableVector.h ../include/SimpleStats.h ../include/TrimSequence.h ../include/UnitTest.h
ar d ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
ranlib ../libStatGen.a
ar d ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o
ranlib ../libStatGen_debug.a
ar d ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o
ranlib ../libStatGen_profile.a
rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ 
rm -rf obj inputFileTest *~ results/*
rm -rf obj cigarRollerTest *~ results/*
rm -rf obj memoryMapArrayTest *~ results/*
rm -rf obj stringTest *~ results/*
rm -rf obj packedVectorTest *~ results/*
rm -rf obj nonOverlapRegionsTest *~ results/*
rm -rf obj referenceSequenceTest *~ results/*
rm -rf obj baseUtilitiesTest *~ results/*
rm -rf obj trimSequence *~ results/*
rm -rf obj reusableVectorTest *~ results/*
# clean current directory
rm -f *.o *~
rm -f phiX-bs.umfa phiX-cs.umfa gtest
make[2]: Leaving directory '/<<PKGBUILDDIR>>/general'
make[2]: Entering directory '/<<PKGBUILDDIR>>/bam'
make[2]: Entering directory '/<<PKGBUILDDIR>>/fastq'
make[2]: Entering directory '/<<PKGBUILDDIR>>/glf'
make[2]: Entering directory '/<<PKGBUILDDIR>>/vcf'
rm -f  ../include/FastQFile.h ../include/BaseCount.h ../include/BaseComposition.h ../include/FastQStatus.h
rm -f  ../include/GlfException.h ../include/GlfFile.h ../include/GlfHeader.h ../include/GlfRecord.h ../include/GlfRefSection.h ../include/GlfStatus.h
ar d ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
ar d ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
ranlib ../libStatGen.a
rm -f  ../include/VcfFile.h ../include/VcfFileReader.h ../include/VcfFileWriter.h ../include/VcfGenotypeField.h ../include/VcfGenotypeFormat.h ../include/VcfGenotypeSample.h ../include/VcfHeader.h ../include/VcfHelper.h ../include/VcfRecord.h ../include/VcfRecordField.h ../include/VcfRecordFilter.h ../include/VcfRecordGenotype.h ../include/VcfRecordInfo.h ../include/VcfSubsetSamples.h ../include/VcfRecordDiscardRules.h
ranlib ../libStatGen.a
ar d ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o
ar d ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o
ranlib ../libStatGen.a
rm -f  ../include/SamFileHeader.h ../include/SamFile.h ../include/GenericSamInterface.h ../include/SamInterface.h ../include/BamInterface.h ../include/SamRecord.h ../include/BamIndex.h ../include/SamHeaderHD.h ../include/SamHeaderPG.h ../include/SamHeaderRecord.h ../include/SamHeaderSQ.h ../include/SamHeaderRG.h ../include/SamHeaderTag.h ../include/SamValidation.h ../include/SamStatistics.h ../include/SamQuerySeqWithRefHelper.h ../include/SamFilter.h ../include/PileupElement.h ../include/PileupElementBaseQual.h ../include/SamReferenceInfo.h ../include/SamTags.h ../include/PosList.h ../include/CigarHelper.h ../include/SamRecordPool.h ../include/SamCoordOutput.h ../include/SamRecordHelper.h ../include/Pileup.h ../include/SamHelper.h ../include/SamFlag.h ../include/SamStatus.h
ranlib ../libStatGen_debug.a
ar d ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o
ar d ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
ar d ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o obj/debug/VcfRecordDiscardRules.o
ar d ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o
ranlib ../libStatGen.a
ranlib ../libStatGen_debug.a
ranlib ../libStatGen_debug.a
ranlib ../libStatGen_profile.a
ar d ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o
ar d ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o
ar d ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o obj/profile/VcfRecordDiscardRules.o
rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ 
ranlib ../libStatGen_debug.a
ranlib ../libStatGen_profile.a
ranlib ../libStatGen_profile.a
ar d ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o
ranlib ../libStatGen_profile.a
rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ 
rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ 
rm -f obj/*.o obj/debug/*.o obj/profile/*.o *~ 
rm -rf obj fastqTest *~ results/*
rm -rf obj glfTest *~ results/*
rm -rf obj vcfTest *~ results/*
make[2]: Leaving directory '/<<PKGBUILDDIR>>/fastq'
rm -rf obj samTest *~ results/*
make[2]: Leaving directory '/<<PKGBUILDDIR>>/glf'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/vcf'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/bam'
rm -f libStatGen.a
rm -f libStatGen_debug.a
rm -f libStatGen_profile.a
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
 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
	make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>/samtools'
ln -s ../samtools/bgzf.h ../include/bgzf.h
ln -s ../samtools/knetfile.h ../include/knetfile.h
ln -s ../samtools/khash.h ../include/khash.h
ln -s ../samtools/bam.h ../include/bam.h
mkdir -p obj
gcc -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/bgzf.o -c bgzf.c 
gcc -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/knetfile.o -c knetfile.c 
ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/<<PKGBUILDDIR>>/samtools'
make[3]: Entering directory '/<<PKGBUILDDIR>>/general'
ln -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h
ln -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h
ln -s ../general/BaseUtilities.h ../include/BaseUtilities.h
ln -s ../general/BasicHash.h ../include/BasicHash.h
ln -s ../general/BgzfFileType.h ../include/BgzfFileType.h
ln -s ../general/BgzfFileTypeRecovery.h ../include/BgzfFileTypeRecovery.h
ln -s ../general/CharBuffer.h ../include/CharBuffer.h
ln -s ../general/Chromosome.h ../include/Chromosome.h
ln -s ../general/Cigar.h ../include/Cigar.h
ln -s ../general/CigarRoller.h ../include/CigarRoller.h
ln -s ../general/Error.h ../include/Error.h
ln -s ../general/ErrorHandler.h ../include/ErrorHandler.h
ln -s ../general/FileType.h ../include/FileType.h
ln -s ../general/FortranFormat.h ../include/FortranFormat.h
ln -s ../general/GenomeSequence.h ../include/GenomeSequence.h
ln -s ../general/GenotypeLists.h ../include/GenotypeLists.h
ln -s ../general/glfHandler.h ../include/glfHandler.h
ln -s ../general/GzipFileType.h ../include/GzipFileType.h
ln -s ../general/GzipHeader.h ../include/GzipHeader.h
ln -s ../general/Hash.h ../include/Hash.h
ln -s ../general/IndexBase.h ../include/IndexBase.h
ln -s ../general/Input.h ../include/Input.h
ln -s ../general/InputFile.h ../include/InputFile.h
ln -s ../general/IntArray.h ../include/IntArray.h
ln -s ../general/IntHash.h ../include/IntHash.h
ln -s ../general/LongLongCounter.h ../include/LongLongCounter.h
ln -s ../general/MapFunction.h ../include/MapFunction.h
ln -s ../general/MathMatrix.h ../include/MathMatrix.h
ln -s ../general/MathVector.h ../include/MathVector.h
ln -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h
ln -s ../general/MemoryInfo.h ../include/MemoryInfo.h
ln -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h
ln -s ../general/MemoryMap.h ../include/MemoryMap.h
ln -s ../general/MiniDeflate.h ../include/MiniDeflate.h
ln -s ../general/NonOverlapRegions.h ../include/NonOverlapRegions.h
ln -s ../general/Parameters.h ../include/Parameters.h
ln -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h
ln -s ../general/Pedigree.h ../include/Pedigree.h
ln -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h
ln -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h
ln -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h
ln -s ../general/PedigreePerson.h ../include/PedigreePerson.h
ln -s ../general/PhoneHome.h ../include/PhoneHome.h
ln -s ../general/QuickIndex.h ../include/QuickIndex.h
ln -s ../general/Random.h ../include/Random.h
ln -s ../general/ReferenceSequence.h ../include/ReferenceSequence.h
ln -s ../general/SmithWaterman.h ../include/SmithWaterman.h
ln -s ../general/Sort.h ../include/Sort.h
ln -s ../general/STLUtilities.h ../include/STLUtilities.h
ln -s ../general/StatGenStatus.h ../include/StatGenStatus.h
ln -s ../general/StringAlias.h ../include/StringAlias.h
ln -s ../general/StringArray.h ../include/StringArray.h
ln -s ../general/StringBasics.h ../include/StringBasics.h
ln -s ../general/StringHash.h ../include/StringHash.h
ln -s ../general/StringMap.h ../include/StringMap.h
ln -s ../general/Tabix.h ../include/Tabix.h
ln -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h
ln -s ../general/Constant.h ../include/Constant.h
ln -s ../general/CSG_MD5.h ../include/CSG_MD5.h
ln -s ../general/Generic.h ../include/Generic.h
ln -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h
ln -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h
ln -s ../general/InplaceMerge.h ../include/InplaceMerge.h
ln -s ../general/LongHash.h ../include/LongHash.h
ln -s ../general/LongInt.h ../include/LongInt.h
ln -s ../general/MathConstant.h ../include/MathConstant.h
ln -s ../general/PackedVector.h ../include/PackedVector.h
ln -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h
ln -s ../general/Performance.h ../include/Performance.h
ln -s ../general/ReusableVector.h ../include/ReusableVector.h
ln -s ../general/SimpleStats.h ../include/SimpleStats.h
ln -s ../general/TrimSequence.h ../include/TrimSequence.h
ln -s ../general/UnitTest.h ../include/UnitTest.h
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
In file included from /usr/include/c++/8/map:60,
                 from IndexBase.h:23,
                 from IndexBase.cpp:18:
/usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, Chunk>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, Chunk> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, Chunk> >]':
/usr/include/c++/8/bits/stl_tree.h:2486:5: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'Chunk SortedChunkList::pop()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'bool SortedChunkList::mergeOverlapping()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/<<PKGBUILDDIR>>/general'
make[3]: Entering directory '/<<PKGBUILDDIR>>/bam'
make[3]: Entering directory '/<<PKGBUILDDIR>>/fastq'
make[3]: Entering directory '/<<PKGBUILDDIR>>/glf'
make[3]: Entering directory '/<<PKGBUILDDIR>>/vcf'
ln -s ../glf/GlfException.h ../include/GlfException.h
ln -s ../fastq/FastQFile.h ../include/FastQFile.h
ln -s ../glf/GlfFile.h ../include/GlfFile.h
ln -s ../fastq/BaseCount.h ../include/BaseCount.h
ln -s ../glf/GlfHeader.h ../include/GlfHeader.h
ln -s ../fastq/BaseComposition.h ../include/BaseComposition.h
ln -s ../glf/GlfRecord.h ../include/GlfRecord.h
ln -s ../fastq/FastQStatus.h ../include/FastQStatus.h
ln -s ../glf/GlfRefSection.h ../include/GlfRefSection.h
mkdir -p obj
ln -s ../glf/GlfStatus.h ../include/GlfStatus.h
ln -s ../vcf/VcfFile.h ../include/VcfFile.h
mkdir -p obj
ln -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
ln -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\""
ln -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h
ln -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h
ln -s ../bam/SamFileHeader.h ../include/SamFileHeader.h
ln -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h
ln -s ../bam/SamFile.h ../include/SamFile.h
ln -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h
ln -s ../vcf/VcfHeader.h ../include/VcfHeader.h
ln -s ../bam/SamInterface.h ../include/SamInterface.h
ln -s ../vcf/VcfHelper.h ../include/VcfHelper.h
ln -s ../bam/BamInterface.h ../include/BamInterface.h
ln -s ../vcf/VcfRecord.h ../include/VcfRecord.h
ln -s ../bam/SamRecord.h ../include/SamRecord.h
ln -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h
ln -s ../bam/BamIndex.h ../include/BamIndex.h
ln -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h
ln -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h
ln -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h
ln -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h
ln -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h
ln -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h
ln -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h
ln -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h
ln -s ../vcf/VcfRecordDiscardRules.h ../include/VcfRecordDiscardRules.h
ln -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h
mkdir -p obj
ln -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h
ln -s ../bam/SamValidation.h ../include/SamValidation.h
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
ln -s ../bam/SamStatistics.h ../include/SamStatistics.h
ln -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h
ln -s ../bam/SamFilter.h ../include/SamFilter.h
ln -s ../bam/PileupElement.h ../include/PileupElement.h
ln -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h
ln -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h
ln -s ../bam/SamTags.h ../include/SamTags.h
ln -s ../bam/PosList.h ../include/PosList.h
ln -s ../bam/CigarHelper.h ../include/CigarHelper.h
ln -s ../bam/SamRecordPool.h ../include/SamRecordPool.h
ln -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h
ln -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h
ln -s ../bam/Pileup.h ../include/Pileup.h
ln -s ../bam/SamHelper.h ../include/SamHelper.h
ln -s ../bam/SamFlag.h ../include/SamFlag.h
ln -s ../bam/SamStatus.h ../include/SamStatus.h
mkdir -p obj
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/<<PKGBUILDDIR>>/fastq'
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/<<PKGBUILDDIR>>/glf'
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o obj/VcfRecordDiscardRules.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/<<PKGBUILDDIR>>/vcf'
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
g++  -O4 -fPIC -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bam'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
# Build the shared library
g++ -shared -o libStatGen.so.0 */obj/*.o -fPIC -Wl,-soname,libStatGen.so.0 -Wl,-z,relro -Wl,-z,now
# Build doxygen doc
doxygen
warning: Tag `DETAILS_AT_TOP' at line 163 of file `Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `SYMBOL_CACHE_SIZE' at line 296 of file `Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `SHOW_DIRECTORIES' at line 484 of file `Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `HTML_ALIGN_MEMBERS' at line 810 of file `Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `USE_INLINE_TREES' at line 963 of file `Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `XML_SCHEMA' at line 1156 of file `Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `XML_DTD' at line 1162 of file `Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: doxygen no longer ships with the FreeSans font.
You may want to clear or change DOT_FONTNAME.
Otherwise you run the risk that the wrong font is being used for dot generated graphs.
Adding custom extension mapping: .h will be treated as language c++
Notice: Output directory `dox' does not exist. I have created it for you.
Searching for include files...
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Searching for images...
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Searching for files to exclude
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Searching for files in directory /<<PKGBUILDDIR>>/dox/html
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Searching INPUT for files to process...
Searching for files in directory /<<PKGBUILDDIR>>/bam
Searching for files in directory /<<PKGBUILDDIR>>/bam/examples
Searching for files in directory /<<PKGBUILDDIR>>/bam/examples/pileup
Searching for files in directory /<<PKGBUILDDIR>>/bam/examples/printRefPositions
Searching for files in directory /<<PKGBUILDDIR>>/bam/examples/printRefPositions/expected
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Reading and parsing tag files
Parsing files
Preprocessing /<<PKGBUILDDIR>>/bam/BamIndex.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/BamIndex.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/BamIndex.h...
Parsing file /<<PKGBUILDDIR>>/bam/BamIndex.h...
Preprocessing /<<PKGBUILDDIR>>/bam/BamInterface.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/BamInterface.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/BamInterface.h...
Parsing file /<<PKGBUILDDIR>>/bam/BamInterface.h...
Preprocessing /<<PKGBUILDDIR>>/bam/CigarHelper.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/CigarHelper.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/CigarHelper.h...
Parsing file /<<PKGBUILDDIR>>/bam/CigarHelper.h...
Preprocessing /<<PKGBUILDDIR>>/bam/examples/pileup/Main.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/examples/pileup/Main.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/examples/printRefPositions/Main.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/examples/printRefPositions/PrintRefPositions.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/examples/printRefPositions/PrintRefPositions.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/GenericSamInterface.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/GenericSamInterface.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/Pileup.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/PileupElement.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/PileupElement.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/PileupElementBaseQual.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/PileupElementBaseQual.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/PileupElementBaseQual.h...
Parsing file /<<PKGBUILDDIR>>/bam/PileupElementBaseQual.h...
Preprocessing /<<PKGBUILDDIR>>/bam/PosList.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/PosList.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamCoordOutput.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamCoordOutput.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamFile.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamFile.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamFileHeader.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamFileHeader.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamFilter.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamFilter.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamFlag.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamHeaderHD.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamHeaderHD.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamHeaderTag.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamHeaderTag.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamHelper.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamInterface.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamInterface.h...
Parsing file /<<PKGBUILDDIR>>/bam/SamInterface.h...
Preprocessing /<<PKGBUILDDIR>>/bam/SamQuerySeqWithRefHelper.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamQuerySeqWithRefHelper.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamRecord.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamRecord.h...
Parsing file /<<PKGBUILDDIR>>/bam/SamRecord.h...
Preprocessing /<<PKGBUILDDIR>>/bam/SamRecordHelper.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/SamRecordHelper.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/SamRecordHelper.h...
Parsing file /<<PKGBUILDDIR>>/bam/SamRecordHelper.h...
Preprocessing /<<PKGBUILDDIR>>/bam/SamRecordPool.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/SamRecordPool.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/SamRecordPool.h...
Parsing file /<<PKGBUILDDIR>>/bam/SamRecordPool.h...
Preprocessing /<<PKGBUILDDIR>>/bam/SamReferenceInfo.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamReferenceInfo.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamStatistics.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamTags.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/SamTags.h...
Parsing file /<<PKGBUILDDIR>>/bam/SamTags.h...
Preprocessing /<<PKGBUILDDIR>>/bam/SamValidation.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/SamValidation.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/SamValidation.h...
Parsing file /<<PKGBUILDDIR>>/bam/SamValidation.h...
Preprocessing /<<PKGBUILDDIR>>/bam/test/BamIndexTest.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/test/BamIndexTest.h...
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Preprocessing /<<PKGBUILDDIR>>/bam/test/Main.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/test/Modify.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/test/SamFileTest.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/test/SamFileTest.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/test/SamFileTest.h...
Parsing file /<<PKGBUILDDIR>>/bam/test/SamFileTest.h...
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Parsing file /<<PKGBUILDDIR>>/bam/test/ShiftIndels.h...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestCigarHelper.cpp...
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Preprocessing /<<PKGBUILDDIR>>/bam/test/TestEquals.cpp...
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Parsing file /<<PKGBUILDDIR>>/bam/test/TestPileup.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestPileup.h...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestPileup.h...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestPosList.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestPosList.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestPosList.h...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestPosList.h...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestSamCoordOutput.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestSamCoordOutput.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestSamCoordOutput.h...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestSamCoordOutput.h...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestSamRecordHelper.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestSamRecordHelper.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestSamRecordHelper.h...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestSamRecordHelper.h...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestSamRecordPool.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestSamRecordPool.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestSamRecordPool.h...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestSamRecordPool.h...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestValidate.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestValidate.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/test/TestValidate.h...
Parsing file /<<PKGBUILDDIR>>/bam/test/TestValidate.h...
Preprocessing /<<PKGBUILDDIR>>/bam/test/ValidationTest.cpp...
Parsing file /<<PKGBUILDDIR>>/bam/test/ValidationTest.cpp...
Preprocessing /<<PKGBUILDDIR>>/bam/test/ValidationTest.h...
Parsing file /<<PKGBUILDDIR>>/bam/test/ValidationTest.h...
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Sorting lists...
Freeing entry tree
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Building full member lists recursively...
Adding members to member groups.
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ortedChunkList...
Generating docs for compound StatGenStatus...
Generating docs for compound String...
Generating docs for compound StringAlias...
Generating docs for compound StringArray...
Generating docs for compound StringDoubleHash...
Generating docs for compound StringHash...
Generating docs for compound StringHashBase...
Generating docs for compound StringIntHash...
Generating docs for compound StringIntMap...
Generating docs for compound StringMap...
Generating docs for compound StringParameter...
Generating docs for compound SwitchParameter...
Generating docs for compound Tabix...
Generating docs for compound TestPileup...
Generating docs for compound TestPileupElement...
Generating docs for compound TestPosList...
Generating docs for compound TestValidate...
Generating docs for compound TestWrite...
Generating docs for compound Timing...
Generating docs for compound UncompressedFileType...
Generating docs for compound UnitTest...
Generating docs for compound Vector...
Generating docs for compound VectorFunc...
Generating docs for compound Weight...
Generating namespace index...
Generating docs for namespace STLUtilities
Generating graph info page...
Generating directory documentation...
Generating dependency graph for directory bam
Generating dependency graph for directory general/test/dbsnp
Generating dependency graph for directory fastq
Generating dependency graph for directory glf
Generating dependency graph for directory general/test/inputFileTest
Generating dependency graph for directory general/test
Generating index page...
Generating page index...
Generating module index...
Generating namespace index...
Generating namespace member index...
Generating annotated compound index...
Generating alphabetical compound index...
Generating hierarchical class index...
Generating graphical class hierarchy...
Generating member index...
Generating file index...
Generating file member index...
Generating example index...
finalizing index lists...
writing tag file...
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Generating dot graphs using 5 parallel threads...
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lookup cache used 10216/65536 hits=89187 misses=10500
finished...
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -a
	make -j4 test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Entering directory '/<<PKGBUILDDIR>>/samtools'
ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
mkdir -p obj/debug
ar: `u' modifier ignored since `D' is the default (see `U')
mkdir -p obj/profile
gcc -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/bgzf.o -c bgzf.c 
gcc -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/knetfile.o -c knetfile.c 
gcc -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/bgzf.o -c bgzf.c 
gcc -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/knetfile.o -c knetfile.c 
ar -cru ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar -cru ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/<<PKGBUILDDIR>>/samtools'
make[2]: Entering directory '/<<PKGBUILDDIR>>/general'
ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/PhoneHome.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
mkdir -p obj/debug
ar: `u' modifier ignored since `D' is the default (see `U')
mkdir -p obj/profile
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
In file included from /usr/include/c++/8/map:60,
                 from IndexBase.h:23,
                 from IndexBase.cpp:18:
/usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, Chunk>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, Chunk> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, Chunk> >]':
/usr/include/c++/8/bits/stl_tree.h:2486:5: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'Chunk SortedChunkList::pop()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'bool SortedChunkList::mergeOverlapping()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
g++  -ggdb -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
In file included from /usr/include/c++/8/map:60,
                 from IndexBase.h:23,
                 from IndexBase.cpp:18:
/usr/include/c++/8/bits/stl_tree.h: In member function 'void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_erase_aux(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, Chunk>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, Chunk> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, Chunk> >]':
/usr/include/c++/8/bits/stl_tree.h:2486:5: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
     _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'Chunk SortedChunkList::pop()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h: In member function 'bool SortedChunkList::mergeOverlapping()':
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:1141:2: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, Chunk>, std::_Select1st<std::pair<const long long unsigned int, Chunk> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, Chunk> > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, Chunk> >'} changed in GCC 7.1
  _M_erase_aux(__position);
  ^~~~~~~~~~~~
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PhoneHome.o -c PhoneHome.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
g++  -pg -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Werror -Wno-format-truncation  -Wno-strict-overflow  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/PhoneHome.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o
ar: `u' modifier ignored since `D' is the default (see `U')
ar -cru ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/PhoneHome.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o
ar: `u' modifier ignored since `D' is the default (see `U')
mkdir obj
mkdir obj
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/InputFileTest.o -c InputFileTest.cpp -DVERSION="\"0.0.1\""
mkdir obj
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CigarRollerTest.o -c CigarRollerTest.cpp -DVERSION="\"0.0.1\""
mkdir obj
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringTest.o -c StringTest.cpp -DVERSION="\"0.0.1\""
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryMapArrayTest.o -c MemoryMapArrayTest.cpp -DVERSION="\"0.0.1\""
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o  stringTest obj/StringTest.o ../../../libStatGen_debug.a -lm -lz 
mkdir -p results && ./stringTest
mkdir obj
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PackedVectorTest.o -c PackedVectorTest.cpp -DVERSION="\"0.0.1\""
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o  packedVectorTest obj/PackedVectorTest.o ../../../libStatGen_debug.a -lm -lz 
./packedVectorTest
PackedArrayTest PASS: 46  FAIL: 0
mkdir obj
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/ReferenceSequenceTest.o -c ReferenceSequenceTest.cpp -DVERSION="\"0.0.1\""
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o  inputFileTest obj/InputFileTest.o ../../../libStatGen_debug.a -lm -lz 
mkdir -p results && ./inputFileTest > results/results.log && diff data/InputFileTest.bam results/bgzfFile.glf && diff data/InputFileTest.txt results/defaultFile.glf && diff data/InputFileTest.gz results/defaultFile.gz && diff data/InputFileTest.gz results/gzipFile.glf && diff data/InputFileTest.txt results/InputFileTest.glf && diff data/InputFileTest.txt results/uncompressedFile.glf && diff data/textFile.gz results/textFile.gz && diff data/textFile.gz results/textFile1.gz && diff results/results.log expected/results.log
inputFileTest: InputFileTest.cpp:466: void IFILE_Test::test_ifread_ifgetc(const char*): Assertion `readChar == EOF' failed.
Aborted
make[4]: *** [../../../Makefiles/Makefile.test:53: test] Error 134
make[3]: *** [Makefile:24: inputFileTest] Error 2
make[3]: *** Waiting for unfinished jobs....
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o  memoryMapArrayTest obj/MemoryMapArrayTest.o ../../../libStatGen_debug.a -lm -lz 
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o  cigarRollerTest obj/CigarRollerTest.o ../../../libStatGen_debug.a -lm -lz 
mkdir -p results; ./memoryMapArrayTest
MemoryMapArrayTest PASS: 108  FAIL: 0
mkdir -p results; ./cigarRollerTest

CigarRoller PASS: 646  FAIL: 0
g++  -O0 -pipe -Wall -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now  -I../../../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o  referenceSequenceTest obj/ReferenceSequenceTest.o ../../../libStatGen_debug.a -lm -lz 
./referenceSequenceTest
test2 sequence utilization is 6.25% - expect around 6.25%
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
make[4]: *** [../../../Makefiles/Makefile.test:53: test] Aborted
make[3]: *** [Makefile:24: referenceSequenceTest] Error 2
make[2]: *** [../Makefiles/Makefile.common:99: test] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/general'
make[1]: *** [Makefiles/Makefile.base:15: general] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: make -j4 test returned exit code 2
make: *** [debian/rules:11: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2018-10-11T01:11:09Z

Finished
--------


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

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

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

Build Architecture: armhf
Build-Space: 0
Build-Time: 5353
Distribution: buster-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 331
Job: libstatgen_1.0.14-2
Machine Architecture: armhf
Package: libstatgen
Package-Time: 5733
Source-Version: 1.0.14-2
Space: 0
Status: failed
Version: 1.0.14-2
--------------------------------------------------------------------------------
Finished at 2018-10-11T01:11:09Z
Build needed 00:00:00, 0k disc space
Raspbian Package Auto-Building

Build log for libstatgen (1.0.14-2) on armhf
