augustus →
3.3+dfsg-2+b1 →
armhf → 2018-04-10 23:02:11
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| augustus 3.3+dfsg-2+b1 (armhf) Tue, 10 Apr 2018 22:35:12 +0000 |
+==============================================================================+
Package: augustus
Version: 3.3+dfsg-2+b1
Source Version: 3.3+dfsg-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-fef3dee3-7df9-4612-a14a-d93f093deacb' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [10.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [12.4 MB]
Fetched 23.1 MB in 26s (899 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: 'augustus' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/augustus.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 45.7 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main augustus 3.3+dfsg-2 (dsc) [1915 B]
Get:2 http://172.17.0.1/private buster-staging/main augustus 3.3+dfsg-2 (tar) [45.7 MB]
Get:3 http://172.17.0.1/private buster-staging/main augustus 3.3+dfsg-2 (diff) [17.0 kB]
Fetched 45.7 MB in 4s (10.5 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-1cxUmW/augustus-3.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-1cxUmW' 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-8VP0CZ/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-8VP0CZ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-8VP0CZ/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-8VP0CZ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ Packages [429 B]
Fetched 2105 B in 1s (2992 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 e2fsprogs-l10n 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 24 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-8VP0CZ/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 (21.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13952 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 (>= 10), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev, asciidoctor
Filtered Build-Depends: debhelper (>= 10), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive/sbuild-build-depends-augustus-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-augustus-dummy sbuild-build-depends-core-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-8VP0CZ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ Sources [557 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ Packages [637 B]
Fetched 2527 B in 1s (3528 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install augustus 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:
dbus dbus-user-session e2fsprogs-l10n libexpat1 libnss-systemd
libpam-systemd systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
icu-devtools intltool-debian libamd2 libarchive-zip-perl libbam-dev
libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex1.62-dev
libboost-regex1.62.0 libboost1.62-dev libbsd0 libbtf1 libcamd2 libccolamd2
libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcxsparse3
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgraphblas2
libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libhts-dev libhts2
libicu-dev libicu57 libk5crypto3 libkeyutils1 libklu1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libldl2 liblpsolve55-dev
liblzma-dev libmagic-mgc libmagic1 libmetis5 libncurses5-dev libnghttp2-14
libpipeline1 libpsl5 librbio2 librtmp1 libruby2.5 libsigsegv2 libspqr2
libsqlite3-0 libsqlite3-dev libssh2-1 libsuitesparse-dev
libsuitesparseconfig5 libtimedate-perl libtinfo-dev libtool libumfpack5
libxml2 libyaml-0-2 m4 man-db po-debconf rake ruby ruby-did-you-mean
ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.5
rubygems-integration zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make dwz gettext-doc libasprintf-dev libgettextpo-dev groff
libbamtools-doc liblapack-doc libboost1.62-doc libboost-atomic1.62-dev
libboost-chrono1.62-dev libboost-context1.62-dev libboost-coroutine1.62-dev
libboost-date-time1.62-dev libboost-exception1.62-dev libboost-fiber1.62-dev
libboost-filesystem1.62-dev libboost-graph1.62-dev
libboost-graph-parallel1.62-dev libboost-locale1.62-dev libboost-log1.62-dev
libboost-math1.62-dev libboost-mpi1.62-dev libboost-mpi-python1.62-dev
libboost-program-options1.62-dev libboost-python1.62-dev
libboost-random1.62-dev libboost-serialization1.62-dev
libboost-signals1.62-dev libboost-system1.62-dev libboost-test1.62-dev
libboost-thread1.62-dev libboost-timer1.62-dev libboost-type-erasure1.62-dev
libboost-wave1.62-dev libboost1.62-tools-dev libmpfrc++-dev libntl-dev
gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html krb5-doc krb5-user
icu-doc liblzma-doc ncurses-doc sqlite3-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libltdl-dev libmail-sendmail-perl
zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base groff-base
icu-devtools intltool-debian libamd2 libarchive-zip-perl libbam-dev
libbamtools-dev libbamtools2.5.1 libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex1.62-dev
libboost-regex1.62.0 libboost1.62-dev libbsd0 libbtf1 libcamd2 libccolamd2
libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcxsparse3
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgraphblas2
libgsl-dev libgsl23 libgslcblas0 libgssapi-krb5-2 libhts-dev libhts2
libicu-dev libicu57 libk5crypto3 libkeyutils1 libklu1 libkrb5-3
libkrb5support0 liblapack-dev liblapack3 libldl2 liblpsolve55-dev
liblzma-dev libmagic-mgc libmagic1 libmetis5 libncurses5-dev libnghttp2-14
libpipeline1 libpsl5 librbio2 librtmp1 libruby2.5 libsigsegv2 libspqr2
libsqlite3-dev libssh2-1 libsuitesparse-dev libsuitesparseconfig5
libtimedate-perl libtinfo-dev libtool libumfpack5 libxml2 libyaml-0-2 m4
man-db po-debconf rake ruby ruby-did-you-mean ruby-minitest ruby-net-telnet
ruby-power-assert ruby-test-unit ruby2.5 rubygems-integration
sbuild-build-depends-augustus-dummy zlib1g-dev
The following packages will be upgraded:
libsqlite3-0
1 upgraded, 95 newly installed, 0 to remove and 23 not upgraded.
Need to get 22.6 MB/57.9 MB of archives.
After this operation, 325 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8VP0CZ/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [920 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-10 [1005 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.0-1 [24.6 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.2-1 [1145 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libsqlite3-0 armhf 3.23.0-1 [515 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf rubygems-integration all 1.11 [4994 B]
Get:9 http://172.17.0.1/private buster-staging/main armhf rake all 12.3.1-1 [66.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf ruby-did-you-mean all 1.2.0-2 [14.2 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf ruby-minitest all 5.10.3-1 [53.5 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf ruby-power-assert all 0.3.0-1 [7902 B]
Get:14 http://172.17.0.1/private buster-staging/main armhf ruby-test-unit all 3.2.5-1 [71.7 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libyaml-0-2 armhf 0.1.7-2 [39.9 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libruby2.5 armhf 2.5.1-1 [3125 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf ruby2.5 armhf 2.5.1-1 [384 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf ruby armhf 1:2.5.1 [11.3 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf asciidoctor all 1.5.5-1 [183 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-1 [32.2 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3 [736 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.040-1 [18.4 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.040-1 [11.8 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.0-4 [2749 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.1.6 [1009 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libsuitesparseconfig5 armhf 1:5.2.0+dfsg-1 [20.2 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libamd2 armhf 1:5.2.0+dfsg-1 [26.5 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-3 [128 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-3 [21.8 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-12 [191 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-4 [112 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-5 [49.0 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-5 [58.0 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b8 [3694 B]
Get:47 http://172.17.0.1/private buster-staging/main armhf libbtf1 armhf 1:5.2.0+dfsg-1 [20.5 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libcamd2 armhf 1:5.2.0+dfsg-1 [27.1 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libccolamd2 armhf 1:5.2.0+dfsg-1 [27.8 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libcolamd2 armhf 1:5.2.0+dfsg-1 [24.8 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libmetis5 armhf 5.1.0.dfsg-5 [131 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libcholmod3 armhf 1:5.2.0+dfsg-1 [206 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.1-1 [51.4 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libcxsparse3 armhf 1:5.2.0+dfsg-1 [48.6 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf libgraphblas2 armhf 1:5.2.0+dfsg-1 [383 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.4+dfsg-6 [75.1 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.4+dfsg-6 [681 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.4+dfsg-6 [863 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libklu1 armhf 1:5.2.0+dfsg-1 [48.2 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-4 [1564 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libldl2 armhf 1:5.2.0+dfsg-1 [20.4 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libumfpack5 armhf 1:5.2.0+dfsg-1 [125 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf librbio2 armhf 1:5.2.0+dfsg-1 [29.1 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libspqr2 armhf 1:5.2.0+dfsg-1 [64.7 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libsuitesparse-dev armhf 1:5.2.0+dfsg-1 [895 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf liblpsolve55-dev armhf 5.5.0.15-4 [350 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libtinfo-dev armhf 6.1-1 [66.6 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1-1 [152 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.23.0-1 [645 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 22.6 MB in 4s (5148 kB/s)
Selecting previously unselected package libbsd0:armhf.
(Reading database ... 13952 files and directories currently installed.)
Preparing to unpack .../0-libbsd0_0.8.7-1_armhf.deb ...
Unpacking libbsd0:armhf (0.8.7-1) ...
Selecting previously unselected package bsdmainutils.
Preparing to unpack .../1-bsdmainutils_11.1.2_armhf.deb ...
Unpacking bsdmainutils (11.1.2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../2-groff-base_1.22.3-10_armhf.deb ...
Unpacking groff-base (1.22.3-10) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../3-libpipeline1_1.5.0-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.0-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../4-man-db_2.8.2-1_armhf.deb ...
Unpacking man-db (2.8.2-1) ...
Preparing to unpack .../5-libsqlite3-0_3.23.0-1_armhf.deb ...
Unpacking libsqlite3-0:armhf (3.23.0-1) over (3.22.0-2) ...
Setting up libsqlite3-0:armhf (3.23.0-1) ...
Selecting previously unselected package libmagic-mgc.
(Reading database ... 14561 files and directories currently installed.)
Preparing to unpack .../00-libmagic-mgc_1%3a5.32-2_armhf.deb ...
Unpacking libmagic-mgc (1:5.32-2) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../01-libmagic1_1%3a5.32-2_armhf.deb ...
Unpacking libmagic1:armhf (1:5.32-2) ...
Selecting previously unselected package file.
Preparing to unpack .../02-file_1%3a5.32-2_armhf.deb ...
Unpacking file (1:5.32-2) ...
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No schema files found: removed existing output file.
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libssh2-1:armhf (1.8.0-1) ...
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Setting up ruby-net-telnet (0.1.1-2) ...
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Setting up libkeyutils1:armhf (1.5.9-9.2) ...
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
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Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
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Setting up libbtf1:armhf (1:5.2.0+dfsg-1) ...
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Setting up libcxsparse3:armhf (1:5.2.0+dfsg-1) ...
Setting up libgsl23:armhf (2.4+dfsg-6) ...
Setting up gettext (0.19.8.1-6) ...
Setting up libblas-dev:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libgsl-dev (2.4+dfsg-6) ...
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up librbio2:armhf (1:5.2.0+dfsg-1) ...
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Setting up libcamd2:armhf (1:5.2.0+dfsg-1) ...
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Setting up autoconf (2.69-11) ...
Setting up libicu-dev (57.1-9) ...
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Setting up libkrb5support0:armhf (1.16-2) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up libamd2:armhf (1:5.2.0+dfsg-1) ...
Setting up automake (1:1.15.1-3) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.2-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up liblapack-dev:armhf (3.7.1-4) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libtool (2.4.6-2) ...
Setting up libk5crypto3:armhf (1.16-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libboost-regex1.62-dev:armhf (1.62.0+dfsg-5) ...
Setting up libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-5) ...
Setting up libklu1:armhf (1:5.2.0+dfsg-1) ...
Setting up libcholmod3:armhf (1:5.2.0+dfsg-1) ...
Setting up libboost-iostreams-dev:armhf (1.62.0.1+b8) ...
Setting up libkrb5-3:armhf (1.16-2) ...
Setting up libspqr2:armhf (1:5.2.0+dfsg-1) ...
Setting up libumfpack5:armhf (1:5.2.0+dfsg-1) ...
Setting up libgssapi-krb5-2:armhf (1.16-2) ...
Setting up libsuitesparse-dev:armhf (1:5.2.0+dfsg-1) ...
Setting up libcurl3-gnutls:armhf (7.58.0-2) ...
Setting up liblpsolve55-dev (5.5.0.15-4) ...
Setting up libhts2:armhf (1.7-2) ...
Setting up libhts-dev:armhf (1.7-2) ...
Setting up dh-autoreconf (17) ...
Setting up ruby-test-unit (3.2.5-1) ...
Setting up rake (12.3.1-1) ...
Setting up dh-strip-nondeterminism (0.040-1) ...
Setting up debhelper (11.1.6) ...
Setting up libruby2.5:armhf (2.5.1-1) ...
Setting up ruby2.5 (2.5.1-1) ...
Setting up ruby (1:2.5.1) ...
Setting up asciidoctor (1.5.5-1) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.30-8+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-2+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180321-1+rpi1 linux-libc-dev_4.15.11-1+rpi1
Package versions: adduser_3.117 apt_1.6~beta1 asciidoctor_1.5.5-1 autoconf_2.69-11 automake_1:1.15.1-3 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.44 bash_4.4.18-1.1 binutils_2.30-8+rpi1 binutils-arm-linux-gnueabihf_2.30-8+rpi1 binutils-common_2.30-8+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4 bzip2_1.0.6-8.1 ca-certificates_20170717 coreutils_8.28-1 cpio_2.12+dfsg-6 cpp_4:7.2.0-1d1 cpp-7_7.3.0-12 dash_0.5.8-2.10 dbus_1.12.6-2 dbus-user-session_1.12.6-2 debconf_1.5.66 debhelper_11.1.6 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.040-1 diffutils_1:3.6-1 dirmngr_2.2.5-1 dmsetup_2:1.02.145-4.1 dpkg_1.19.0.5 dpkg-dev_1.19.0.5 e2fslibs_1.44.1-1 e2fsprogs_1.44.1-1 e2fsprogs-l10n_1.44.1-1 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.32-2 findutils_4.6.0+git+20171230-2 g++_4:7.2.0-1d1 g++-7_7.3.0-12 gcc_4:7.2.0-1d1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1 gcc-5-base_5.5.0-8 gcc-6-base_6.4.0-12+rpi1 gcc-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180321-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-l10n_2.2.5-1 gnupg-utils_2.2.5-1 gpg_2.2.5-1 gpg-agent_2.2.5-1 gpg-wks-client_2.2.5-1 gpg-wks-server_2.2.5-1 gpgconf_2.2.5-1 gpgsm_2.2.5-1 gpgv_2.2.5-1 grep_3.1-2 groff-base_1.22.3-10 gzip_1.6-5 hostname_3.20 icu-devtools_57.1-9 inetutils-ping_2:1.9.4-3 init-system-helpers_1.51 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-11+rpi1 kmod_25-1 libacl1_2.2.52-3 libamd2_1:5.2.0+dfsg-1 libapparmor1_2.12-4 libapt-pkg5.0_1.6~beta1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-1.1 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180321-1+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.2-1 libaudit1_1:2.8.2-1 libbam-dev_0.1.19-2 libbamtools-dev_2.5.1+dfsg-3 libbamtools2.5.1_2.5.1+dfsg-3 libbinutils_2.30-8+rpi1 libblas-dev_3.7.1-4 libblas3_3.7.1-4 libblkid1_2.31.1-0.5 libboost-iostreams-dev_1.62.0.1+b8 libboost-iostreams1.62-dev_1.62.0+dfsg-5 libboost-iostreams1.62.0_1.62.0+dfsg-5 libboost-regex1.62-dev_1.62.0+dfsg-5 libboost-regex1.62.0_1.62.0+dfsg-5 libboost1.62-dev_1.62.0+dfsg-5 libbsd0_0.8.7-1 libbtf1_1:5.2.0+dfsg-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.27-2+rpi1 libc-dev-bin_2.27-2+rpi1 libc6_2.27-2+rpi1 libc6-dev_2.27-2+rpi1 libcamd2_1:5.2.0+dfsg-1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180321-1+rpi1 libccolamd2_1:5.2.0+dfsg-1 libcholmod3_1:5.2.0+dfsg-1 libcilkrts5_7.3.0-12 libcolamd2_1:5.2.0+dfsg-1 libcom-err2_1.44.1-1 libcroco3_0.6.12-2 libcryptsetup12_2:2.0.2-1 libcryptsetup4_2:1.7.5-1 libcurl3-gnutls_7.58.0-2 libcxsparse3_1:5.2.0+dfsg-1 libdb5.3_5.3.28-13.1 libdbus-1-3_1.12.6-2 libdebconfclient0_0.243 libdevmapper1.02.1_2:1.02.145-4.1 libdpkg-perl_1.19.0.5 libdrm-common_2.4.91-2+rpi1 libdrm2_2.4.91-2+rpi1 libexpat1_2.2.5-3 libext2fs2_1.44.1-1 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.040-1 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180321-1+rpi1 libgcrypt20_1.8.1-4 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran4_7.3.0-12 libglib2.0-0_2.56.0-4 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180321-1+rpi1 libgpg-error0_1.28-2 libgraphblas2_1:5.2.0+dfsg-1 libgsl-dev_2.4+dfsg-6 libgsl23_2.4+dfsg-6 libgslcblas0_2.4+dfsg-6 libgssapi-krb5-2_1.16-2 libhogweed4_3.4-1 libhts-dev_1.7-2 libhts2_1.7-2 libicu-dev_57.1-9 libicu57_57.1-9 libidn11_1.33-2.1 libidn2-0_2.0.4-1.1 libip4tc0_1.6.2-1 libisl15_0.18-4 libjson-c3_0.12.1-1.3 libk5crypto3_1.16-2 libkeyutils1_1.5.9-9.2 libklibc_2.0.4-11+rpi1 libklu1_1:5.2.0+dfsg-1 libkmod2_25-1 libkrb5-3_1.16-2 libkrb5support0_1.16-2 libksba8_1.3.5-2 liblapack-dev_3.7.1-4 liblapack3_3.7.1-4 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libldl2_1:5.2.0+dfsg-1 liblocale-gettext-perl_1.07-3+b2 liblpsolve55-dev_5.5.0.15-4 liblz4-1_0.0~r131-2 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.32-2 libmagic1_1:5.32-2 libmetis5_5.1.0.dfsg-5 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses5_6.1-1 libncurses5-dev_6.1-1 libncursesw5_6.1-1 libnettle6_3.4-1 libnghttp2-14_1.31.0-1 libnpth0_1.5-3 libnss-systemd_238-3 libp11-kit0_0.23.9-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-3 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.26_5.26.1-5 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.12-4 libpsl5_0.20.1-1 librbio2_1:5.2.0+dfsg-1 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libruby2.5_2.5.1-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-1 libsmartcols1_2.31.1-0.5 libspqr2_1:5.2.0+dfsg-1 libsqlite3-0_3.23.0-1 libsqlite3-dev_3.23.0-1 libss2_1.44.1-1 libssh2-1_1.8.0-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180321-1+rpi1 libsuitesparse-dev_1:5.2.0+dfsg-1 libsuitesparseconfig5_1:5.2.0+dfsg-1 libsystemd0_238-3 libtasn1-6_4.13-2 libtext-charwidth-perl_0.04-7.1 libtext-iconv-perl_1.7-5+b9 libtext-wrapi18n-perl_0.06-7.1 libtimedate-perl_2.3000-2 libtinfo-dev_6.1-1 libtinfo5_6.1-1 libtool_2.4.6-2 libubsan0_7.3.0-12 libudev1_238-3 libumfpack5_1:5.2.0+dfsg-1 libunistring2_0.9.8-1 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 libyaml-0-2_0.1.7-2 linux-base_4.5 linux-libc-dev_4.15.11-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.2-1 mawk_1.3.3-17 mount_2.31.1-0.5 multiarch-support_2.27-2+rpi1 nano_2.9.4-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-1 perl_5.26.1-5 perl-base_5.26.1-5 perl-modules-5.26_5.26.1-5 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.12-4 rake_12.3.1-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 ruby_1:2.5.1 ruby-did-you-mean_1.2.0-2 ruby-minitest_5.10.3-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.3.0-1 ruby-test-unit_3.2.5-1 ruby2.5_2.5.1-1 rubygems-integration_1.11 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-2 sensible-utils_0.0.12 systemd_238-3 systemd-sysv_238-3 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-3 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Fri Jul 28 21:37:54 2017 UTC
gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./augustus_3.3+dfsg-2.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.3+dfsg
dpkg-source: info: unpacking augustus_3.3+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.3+dfsg-2.debian.tar.xz
dpkg-source: info: applying search_config_path
dpkg-source: info: applying set_installdir
dpkg-source: info: applying keep_cflags
dpkg-source: info: applying buildflags.patch
dpkg-source: info: applying spelling.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 3.3+dfsg-2+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
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-fef3dee3-7df9-4612-a14a-d93f093deacb
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.3+dfsg-2+b1
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build augustus-3.3+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping'
(cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping/src'
/bin/sh: 1: cd: can't cd to ../../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/joingenes'
rm -rf *o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2wig'
rm -f bam2wig bam2wig.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/checkTargetSortedness'
rm -f *.o checkTargetSortedness
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/compileSpliceCands'
rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam'
(cd src; make clean; cd ../bin; rm -f filterBam; cd ../../../bin; rm -f filterBam)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam/src'
rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam/src'
/bin/sh: 1: cd: can't cd to ../../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam'
rm -rf bin
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
dh_clean
debian/rules build-arch
dh build-arch --parallel
dh_update_autotools_config -a -O--parallel
dh_autoreconf -a -O--parallel
dh_auto_configure -a -O--parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/aln2wig'
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -c aln2wig.c
gcc -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o;
cp aln2wig ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2hints'
g++ -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz
cp bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2wig'
cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/tabix/ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c bam2wig.c -o bam2wig.o -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/tabix/
cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/tabix/ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig /usr/lib/libbam.a -lhts -lcurses -lm -lz -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/checkTargetSortedness'
cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c checkTargetSortedness.c -o checkTargetSortedness.o -I/usr/include/samtools -I.
cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now checkTargetSortedness.o -o checkTargetSortedness -lbam -lcurses -lm -lz -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/compileSpliceCands'
cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90
s = malloc(3500000000);
^
compileSpliceCands.c:226:4: warning: argument 1 value '3500000000' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
s = malloc(3500000000);
~~^~~~~~~~~~~~~~~~~~~~
In file included from compileSpliceCands.c:14:0:
/usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here
extern void *malloc (size_t __size) __THROW __attribute_malloc__ __wur;
^~~~~~
compileSpliceCands.c: In function 'parseList':
compileSpliceCands.c:350:32: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
findPossibleSpliceSites(left->name,actualChromosome,left->startPos,left->endPos,right->startPos,right->endPos,left->strand,right->strand);
^~~~
compileSpliceCands.c: In function 'main':
compileSpliceCands.c:563:3: warning: 'chromosomeLength' may be used uninitialized in this function [-Wmaybe-uninitialized]
parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -o compileSpliceCands compileSpliceCands.o list.o -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now;
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
cp filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping/src'
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o gene.o gene.cc -I../include
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o genome.o genome.cc -I../include
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o homGeneMapping main.cc gene.o genome.o -I../include -Wl,-z,relro -Wl,-z,now
cp homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/joingenes'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_transcript.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_ios.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.o jg_transcript.o jg_ios.o -o joingenes -Wl,-z,relro -Wl,-z,now
cp joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/joingenes'
dh_auto_build
make -j4 -O
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
mkdir -p bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o pp_hitseq.o pp_hitseq.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o properties.o properties.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o pp_profile.o pp_profile.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PP::Column; _Alloc = std::allocator<PP::Column>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<PP::Column>::iterator {aka __gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'PP::Block::Block(PP::DistanceType, const std::vector<std::__cxx11::basic_string<char> >&, std::__cxx11::string)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PP::Block; _Alloc = std::allocator<PP::Block>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<PP::Block>::iterator {aka __gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool PP::Block::initThresholds()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void PP::Profile::calcGlobalThresh(const std::vector<std::vector<Dist> >&)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void PP::Profile::parse_stream(std::istream&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::_Alloc_node; _Key = int; _Val = std::pair<const int, LLDouble>; _KeyOfValue = std::_Select1st<std::pair<const int, LLDouble> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/7/bits/stl_tree.h:2191:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/7/bits/stl_vector.h: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/geneticcode.hh:17,
from ../include/pp_profile.hh:21,
from pp_profile.cc:14:
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o pp_scoring.o pp_scoring.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PP::BonusProbEntry; _Alloc = std::allocator<PP::BonusProbEntry>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<PP::BonusProbEntry>::iterator {aka __gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from ../include/pp_scoring.hh:21,
from pp_scoring.cc:14:
/usr/include/c++/7/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, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/7/bits/stl_tree.h:2484:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h:2484:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
/usr/include/c++/7/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::size_type std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::erase(const _Key&) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/7/bits/stl_tree.h:2502:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
_M_erase_aux(__p.first, __p.second);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::_Alloc_node; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/7/bits/stl_tree.h:2191:7: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In member function 'void ViterbiSubmapType::eraseAndDecCounts(ViterbiSubmapType::iterator) const':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h: In member function 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)':
/usr/include/c++/7/bits/stl_tree.h:1159:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
{ _M_erase_aux(__first, __last); }
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h: In member function 'bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h: In member function 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h: In member function 'void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h: In member function 'void PP::BonusProbType::mergeIntoSubmap(int, ViterbiSubmapType&, SubstateIdMap*)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)':
/usr/include/c++/7/bits/stl_tree.h:1159:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
{ _M_erase_aux(__first, __last); }
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)':
/usr/include/c++/7/bits/stl_tree.h:1159:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
{ _M_erase_aux(__first, __last); }
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o genbank.o genbank.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o statemodel.o statemodel.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from statemodel.cc:16:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator {aka __gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from statemodel.cc:16:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void StateModel::initPredecessors(Matrix<LLDouble>&, int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o types.o types.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from types.cc:18:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from types.cc:18:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void Constant::init()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'Double quantile(const std::vector<LLDouble>&, float)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o namgene.o namgene.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o motif.o motif.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from motif.cc:14:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from motif.cc:14:
/usr/include/c++/7/bits/stl_vector.h: In member function 'Double Motif::getProbThreshold(double, int)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o evaluation.o evaluation.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o geneticcode.o geneticcode.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o projectio.o projectio.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o hints.o hints.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o gene.o gene.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/list:64:0,
from ../include/vitmatrix.hh:19,
from ../include/pp_scoring.hh:21,
from ../include/gene.hh:15,
from gene.cc:21:
/usr/include/c++/7/bits/list.tcc: In member function 'void std::__cxx11::list<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = std::_List_const_iterator<PP::Match>; _Tp = PP::Match; _Alloc = std::allocator<PP::Match>]':
/usr/include/c++/7/bits/list.tcc:307:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
list<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/list.tcc:307:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/7/bits/list.tcc: In copy constructor 'Gene::Gene(const Gene&)':
/usr/include/c++/7/bits/list.tcc:285:22: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/list.tcc: In static member function 'static StatePath* StatePath::condenseStatePath(StatePath*)':
/usr/include/c++/7/bits/list.tcc:285:22: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/geneticcode.hh:17,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../include/types.hh:37,
from ../include/geneticcode.hh:17,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/geneticcode.hh:17,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/7/bits/stl_vector.h: In function 'void examineBaseCountOfGeneSeq(AnnoSequence*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/geneticcode.hh:17,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o intronmodel.o intronmodel.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void IntronModel::readProbabilities(int)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void IntronModel::readAllParameters()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o exonmodel.o exonmodel.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/exonmodel.hh:22,
from exonmodel.cc:25:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/exonmodel.hh:22,
from exonmodel.cc:25:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void ExonModel::readAllParameters()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o igenicmodel.o igenicmodel.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/igenicmodel.hh:20,
from igenicmodel.cc:14:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/igenicmodel.hh:20,
from igenicmodel.cc:14:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void IGenicModel::readProbabilities(int)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void IGenicModel::readAllParameters()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o vitmatrix.o vitmatrix.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = ViterbiSubmapType; _Alloc = std::allocator<ViterbiSubmapType>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<ViterbiSubmapType>::iterator {aka __gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = ViterbiEntryType; _Alloc = std::allocator<ViterbiEntryType>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<ViterbiEntryType>::iterator {aka __gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >}' changed in GCC 7.1
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<ViterbiEntryType>::iterator {aka __gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void ViterbiColumnType::addState(int, signed char)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/7/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, std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/7/bits/stl_tree.h:2484:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h:2484:5: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
/usr/include/c++/7/bits/stl_tree.h: In member function 'void ViterbiSubmapType::useMaximum(Double&)':
/usr/include/c++/7/bits/stl_tree.h:1159:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
{ _M_erase_aux(__first, __last); }
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h:1159:21: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
{ _M_erase_aux(__first, __last); }
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In member function 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)':
/usr/include/c++/7/bits/stl_tree.h:2502:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
_M_erase_aux(__p.first, __p.second);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::_Alloc_node; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/7/bits/stl_tree.h:2191:7: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_tree.h: In member function 'void ViterbiSubmapType::merge(ViterbiSubmapType&, Double)':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h: In member function 'void ViterbiSubmapType::registerPredecessors()':
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o lldouble.o lldouble.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o extrinsicinfo.o extrinsicinfo.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::_Alloc_node; _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity<Feature>; _Compare = std::less<Feature>; _Alloc = std::allocator<Feature>]':
/usr/include/c++/7/bits/stl_tree.h:2191:7: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_algo.h: In function '_OutputIterator std::__set_difference(_InputIterator1, _InputIterator1, _InputIterator2, _InputIterator2, _OutputIterator, _Compare) [with _InputIterator1 = std::_Rb_tree_const_iterator<Feature>; _InputIterator2 = std::_Rb_tree_const_iterator<Feature>; _OutputIterator = std::insert_iterator<std::set<Feature> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:5330:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__set_difference(_InputIterator1 __first1, _InputIterator1 __last1,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:5330:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5330:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5330:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h:1072:43: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' changed in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/7/bits/stl_tree.h: In member function 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)':
/usr/include/c++/7/bits/stl_tree.h:2452:21: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' changed in GCC 7.1
_M_insert_unique_(end(), *__first, __an);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_tree.h:2452:21: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' changed in GCC 7.1
_M_insert_unique_(end(), *__first, __an);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_tree.h:2452:21: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' changed in GCC 7.1
_M_insert_unique_(end(), *__first, __an);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from /usr/include/c++/7/map:60:0,
from ../include/types.hh:38,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_tree.h:2452:21: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' changed in GCC 7.1
_M_insert_unique_(end(), *__first, __an);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5395:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void FeatureCollection::readTypeInfo(std::istream&)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o utrmodel.o utrmodel.cc -I../include
utrmodel.cc: In member function 'Double UtrModel::notEndPartEmiProb(int, int, int, Feature*) const':
utrmodel.cc:1468:29: warning: enum constant in boolean context [-Wint-in-bool-context]
if ((utype == utr3init || utr3single || utype == rutr5term || rutr5single) && (part->start < beginOfBioExon && part->end == endOfBioExon) ){
^~~~~~~~~~
utrmodel.cc:1468:65: warning: enum constant in boolean context [-Wint-in-bool-context]
if ((utype == utr3init || utr3single || utype == rutr5term || rutr5single) && (part->start < beginOfBioExon && part->end == endOfBioExon) ){
^~~~~~~~~~~
utrmodel.cc:1472:30: warning: enum constant in boolean context [-Wint-in-bool-context]
if ((utype == rutr3init || rutr3single || utype == utr5term || utr5single) && (part->start == beginOfBioExon && part->end > endOfBioExon) ){
^~~~~~~~~~~
utrmodel.cc:1472:66: warning: enum constant in boolean context [-Wint-in-bool-context]
if ((utype == rutr3init || rutr3single || utype == utr5term || utr5single) && (part->start == beginOfBioExon && part->end > endOfBioExon) ){
^~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, std::vector<_Tp, _Alloc>::value_type) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o mea.o mea.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from ../include/mea.hh:4,
from mea.cc:1:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from ../include/mea.hh:4,
from mea.cc:1:
/usr/include/c++/7/bits/stl_vector.h: In constructor 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o meaPath.o meaPath.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o merkmal.o merkmal.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void BinnedMMGroup::read(std::ifstream&)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void Parameters::addMerkmal(Double*, double)':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Val_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Distance = int; _Tp = LLDouble; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In member function 'void BinnedMMGroup::trainBins(int)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algo.h:61:0,
from /usr/include/c++/7/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/7/algorithm:62:0,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In static member function 'static std::vector<double> CRF::capOutliers(std::vector<double>)':
/usr/include/c++/7/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = int; V = double]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
merkmal.cc: In static member function 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)':
merkmal.cc:338:6: warning: '%d' directive writing between 1 and 10 bytes into a region of size 4 [-Wformat-overflow=]
void CRF::onlineLargeMarginTraining(Parameters* parameters, vector<AnnoSequence*> trainGenes, FeatureCollection &extrinsicFeatures){
^~~
merkmal.cc:338:6: note: directive argument in the range [1, 2147483647]
In file included from /usr/include/stdio.h:862:0,
from /usr/include/c++/7/cstdio:42,
from /usr/include/c++/7/fstream:41,
from ../include/projectio.hh:23,
from ../include/geneticcode.hh:18,
from ../include/motif.hh:21,
from ../include/gene.hh:14,
from ../include/extrinsicinfo.hh:25,
from ../include/merkmal.hh:17,
from merkmal.cc:13:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:34:43: note: '__builtin___sprintf_chk' output between 2 and 11 bytes into a destination of size 4
__bos (__s), __fmt, __va_arg_pack ());
^
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void CRF::improvedIterativeScaling(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o fasta.o fasta.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o exoncand.o exoncand.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o graph.o graph.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o commontrain.o commontrain.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/types.hh:35,
from ../include/commontrain.hh:14,
from commontrain.cc:10:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
In file included from /usr/include/c++/7/vector:64:0,
from ../include/types.hh:35,
from ../include/commontrain.hh:14,
from commontrain.cc:10:
/usr/include/c++/7/bits/stl_vector.h: In member function 'int Smooth::geoCutOff(const std::vector<long int>&, std::vector<LLDouble>&)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o igenictrain.o igenictrain.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/igenicmodel.hh:20,
from igenictrain.cc:13:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/igenicmodel.hh:20,
from igenictrain.cc:13:
/usr/include/c++/7/bits/stl_vector.h: In member function 'virtual void IGenicModel::buildModel(const AnnoSequence*, int)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o ncmodel.o ncmodel.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/ncmodel.hh:15,
from ncmodel.cc:13:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/ncmodel.hh:15,
from ncmodel.cc:13:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void NcModel::computeLengthDistributions()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o introntrain.o introntrain.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from introntrain.cc:14:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from introntrain.cc:14:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void IntronModel::makeDSSProbs()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void IntronModel::buildProbabilities(const AnnoSequence*)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o randseqaccess.o randseqaccess.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o dummy.o dummy.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT" > cxxflags
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
cp prepareAlign ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o exontrain.o exontrain.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/exonmodel.hh:22,
from exontrain.cc:13:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:399:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/exonmodel.hh:22,
from exontrain.cc:13:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void ExonModel::computeLowerOrderPats()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void ExonModel::buildProbabilities()':
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:948:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -o utrtrain.o utrtrain.cc -I../include
In file included from /usr/include/c++/7/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrtrain.cc:15:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:458:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrtrain.cc:15:
/usr/include/c++/7/bits/stl_vector.h: In member function 'void UtrModel::buildTSSModel(const AnnoSequence*)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In member function 'void UtrModel::buildProbabilities(const AnnoSequence*)':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h: In static member function 'static void UtrModel::computeLengthDistributions()':
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_vector.h:732:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_fill_insert(end(), __new_size - size(), __x);
~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -Wl,-z,relro -Wl,-z,now -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -I../include -lboost_iostreams
cp fastBlockSearch ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -Wl,-z,relro -Wl,-z,now -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o dummy.o -I../include -lboost_iostreams
cp augustus ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -DZIPINPUT -Wl,-z,relro -Wl,-z,now -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o -I../include -lboost_iostreams
cp etraining ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2hints'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/bam2hints'
make[4]: 'bam2hints' is up to date.
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/compileSpliceCands'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/compileSpliceCands'
make[4]: 'compileSpliceCands' is up to date.
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam'
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam/src'
filterBam compiled with BAMTOOLS=/usr/include/bamtools
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam/src'
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam/src'
cp filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping'
(cd src; make)
make[5]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/joingenes'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs/joingenes'
make[4]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg/auxprogs'
asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
dh_auto_test -a -O--parallel
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
mkdir -p debian/augustus/usr/bin
install bin/* debian/augustus/usr/bin
install auxprogs/checkTargetSortedness/checkTargetSortedness \
debian/augustus/usr/bin
install auxprogs/bam2wig/bam2wig \
debian/augustus/usr/bin
install auxprogs/compileSpliceCands/compileSpliceCands \
debian/augustus/usr/bin
install auxprogs/homGeneMapping/src/homGeneMapping \
debian/augustus/usr/bin
install auxprogs/joingenes/joingenes \
debian/augustus/usr/bin
mkdir -p debian/augustus/usr/share/augustus
cp -r scripts debian/augustus/usr/share/augustus
chmod -R -x debian/augustus/usr/share/augustus/scripts/*
rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \
debian/augustus/usr/share/augustus/scripts/aln2wig
chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \
debian/augustus/usr/share/augustus/scripts/*.pl*
mkdir -p debian/augustus-doc/usr/share/doc/augustus
cp README* debian/augustus-doc/usr/share/doc/augustus
cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial \
debian/augustus-doc/usr/share/doc/augustus
mkdir -p debian/augustus-data/usr/share/augustus
cp -r config debian/augustus-data/usr/share/augustus
find debian/augustus-data/usr/share/augustus \
-type f -exec chmod -x {} \;
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
dh_installdocs -a -O--parallel
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
dh_installchangelogs -k HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
dh_installman -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3+dfsg'
dh_fixperms -a -O--parallel
dh_missing -a -O--parallel
dh_strip -a -O--parallel
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: debian/augustus/usr/bin/fastBlockSearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/filterBam contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/homGeneMapping contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/prepareAlign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness debian/augustus/usr/bin/bam2wig were not linked against libtinfo.so.5 (they use none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/bam2wig was not linked against libhts.so.2 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness debian/augustus/usr/bin/bam2wig were not linked against libncurses.so.5 (they use none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.3+dfsg-2+b1_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.3+dfsg-2+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../augustus_3.3+dfsg-2+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build augustus-3.3+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-04-10T23:01:03Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.3+dfsg-2+b1_armhf.changes:
-------------------------------------
Format: 1.8
Date: Fri, 28 Jul 2017 21:32:29 +0200
Source: augustus (3.3+dfsg-2)
Binary: augustus augustus-data augustus-doc
Binary-Only: yes
Architecture: armhf
Version: 3.3+dfsg-2+b1
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
augustus - gene prediction in eukaryotic genomes
augustus-data - data files for AUGUSTUS
augustus-doc - documentation files for AUGUSTUS
Changes:
augustus (3.3+dfsg-2+b1) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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ca77a20a4cc5c3c07de9bf97b60bbd89722e8824 895372 augustus_3.3+dfsg-2+b1_armhf.deb
Checksums-Sha256:
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Files:
0c8e95073bc89179b4b991d597313555 14559176 debug optional augustus-dbgsym_3.3+dfsg-2+b1_armhf.deb
fd19557cdb47995f11f0b24c7d031c91 7276 science optional augustus_3.3+dfsg-2+b1_armhf.buildinfo
cfb4c3ce33d58cf59182ef0aadcc80f8 895372 science optional augustus_3.3+dfsg-2+b1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.3+dfsg-2+b1_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 14559176 bytes: control archive=1124 bytes.
894 bytes, 13 lines control
1272 bytes, 12 lines md5sums
Package: augustus-dbgsym
Source: augustus (3.3+dfsg-2)
Version: 3.3+dfsg-2+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 14906
Depends: augustus (= 3.3+dfsg-2+b1)
Built-Using: samtools-legacy (= 0.1.19-2)
Section: debug
Priority: optional
Description: debug symbols for augustus
Build-Ids: 1ee5d8c982930de3c34c1abadcf2ecb547a31aea 2a9e0ffa3ae3359d983632019ed5a090eedab707 2e27bcc5bf5cec6919e20552d435c0ab1d28f4e0 3492b1adb213bc78f286fd4f29bdb74b6e0c4260 4c7e4145e0a44d35e8c96481821c6b6bbc1e9c7d 5cd0fafe1222b3d555d752cd560952423a6aacaf 5d141897948046e9c92ff4f9eb3db9fe5a95a9c5 90dbca4c8a42163d13b80cd1f14ca18486e2a0b1 abcd72bca7f2b46fc22a02815d5a3ca7cc9b8aa4 bf30e6eaeebe4f0db31d1433347d10e1c2d9bf90 da06fb48c97ca82d4b71961f0cc2073e3ad5f942 dbf70cd3b9c8a9a217f470bd58dc77b69d117520
drwxr-xr-x root/root 0 2017-07-28 19:32 ./
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/1e/
-rw-r--r-- root/root 894996 2017-07-28 19:32 ./usr/lib/debug/.build-id/1e/e5d8c982930de3c34c1abadcf2ecb547a31aea.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/2a/
-rw-r--r-- root/root 597260 2017-07-28 19:32 ./usr/lib/debug/.build-id/2a/9e0ffa3ae3359d983632019ed5a090eedab707.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/2e/
-rw-r--r-- root/root 13208 2017-07-28 19:32 ./usr/lib/debug/.build-id/2e/27bcc5bf5cec6919e20552d435c0ab1d28f4e0.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 140788 2017-07-28 19:32 ./usr/lib/debug/.build-id/34/92b1adb213bc78f286fd4f29bdb74b6e0c4260.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/4c/
-rw-r--r-- root/root 655732 2017-07-28 19:32 ./usr/lib/debug/.build-id/4c/7e4145e0a44d35e8c96481821c6b6bbc1e9c7d.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/5c/
-rw-r--r-- root/root 644408 2017-07-28 19:32 ./usr/lib/debug/.build-id/5c/d0fafe1222b3d555d752cd560952423a6aacaf.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/5d/
-rw-r--r-- root/root 5716880 2017-07-28 19:32 ./usr/lib/debug/.build-id/5d/141897948046e9c92ff4f9eb3db9fe5a95a9c5.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/90/
-rw-r--r-- root/root 6402660 2017-07-28 19:32 ./usr/lib/debug/.build-id/90/dbca4c8a42163d13b80cd1f14ca18486e2a0b1.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/ab/
-rw-r--r-- root/root 111048 2017-07-28 19:32 ./usr/lib/debug/.build-id/ab/cd72bca7f2b46fc22a02815d5a3ca7cc9b8aa4.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/bf/
-rw-r--r-- root/root 18512 2017-07-28 19:32 ./usr/lib/debug/.build-id/bf/30e6eaeebe4f0db31d1433347d10e1c2d9bf90.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/da/
-rw-r--r-- root/root 18312 2017-07-28 19:32 ./usr/lib/debug/.build-id/da/06fb48c97ca82d4b71961f0cc2073e3ad5f942.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/lib/debug/.build-id/db/
-rw-r--r-- root/root 22140 2017-07-28 19:32 ./usr/lib/debug/.build-id/db/f70cd3b9c8a9a217f470bd58dc77b69d117520.debug
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/doc/
lrwxrwxrwx root/root 0 2017-07-28 19:32 ./usr/share/doc/augustus-dbgsym -> augustus
augustus_3.3+dfsg-2+b1_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 895372 bytes: control archive=4368 bytes.
1344 bytes, 23 lines control
8926 bytes, 119 lines md5sums
Package: augustus
Source: augustus (3.3+dfsg-2)
Version: 3.3+dfsg-2+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3865
Depends: libbamtools2.5.1, libboost-iostreams1.62.0, libc6 (>= 2.15), libgcc1 (>= 1:4.0), libhts2 (>= 1.0), libncurses5 (>= 6), libstdc++6 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3), augustus-data
Built-Using: samtools-legacy (= 0.1.19-2)
Section: science
Priority: optional
Homepage: http://bioinf.uni-greifswald.de/augustus/
Description: gene prediction in eukaryotic genomes
AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences
that is based on a generalized hidden Markov model (HMM), a probabilistic
model of a sequence and its gene structure. After learning gene structures
from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new
sequence and annotates it with the regions of identified genes. External hints,
e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide
and improve the gene finding process. The result is the set of most likely gene
structures that comply with all given user constraints, if such gene
structures exist.
AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts
to train custom models using annotated genomes.
drwxr-xr-x root/root 0 2017-07-28 19:32 ./
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/bin/
-rwxr-xr-x root/root 9684 2017-07-28 19:32 ./usr/bin/aln2wig
-rwxr-xr-x root/root 1089788 2017-07-28 19:32 ./usr/bin/augustus
-rwxr-xr-x root/root 26540 2017-07-28 19:32 ./usr/bin/bam2hints
-rwxr-xr-x root/root 96748 2017-07-28 19:32 ./usr/bin/bam2wig
-rwxr-xr-x root/root 88504 2017-07-28 19:32 ./usr/bin/checkTargetSortedness
-rwxr-xr-x root/root 13780 2017-07-28 19:32 ./usr/bin/compileSpliceCands
-rwxr-xr-x root/root 1237244 2017-07-28 19:32 ./usr/bin/etraining
-rwxr-xr-x root/root 225100 2017-07-28 19:32 ./usr/bin/fastBlockSearch
-rwxr-xr-x root/root 144932 2017-07-28 19:32 ./usr/bin/filterBam
-rwxr-xr-x root/root 108264 2017-07-28 19:32 ./usr/bin/homGeneMapping
-rwxr-xr-x root/root 116232 2017-07-28 19:32 ./usr/bin/joingenes
-rwxr-xr-x root/root 30236 2017-07-28 19:32 ./usr/bin/prepareAlign
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/augustus/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/augustus/scripts/
-rw-r--r-- root/root 12539 2017-07-28 19:32 ./usr/share/augustus/scripts/README.autoAug
-rw-r--r-- root/root 12247 2017-07-28 19:32 ./usr/share/augustus/scripts/SplicedAlignment.pm
-rwxr-xr-x root/root 3022 2017-07-28 19:32 ./usr/share/augustus/scripts/augustus2browser.pl
-rwxr-xr-x root/root 389 2017-07-28 19:32 ./usr/share/augustus/scripts/augustus2gbrowse.pl
-rwxr-xr-x root/root 48984 2017-07-28 19:32 ./usr/share/augustus/scripts/autoAug.pl
-rwxr-xr-x root/root 20477 2017-07-28 19:32 ./usr/share/augustus/scripts/autoAugPred.pl
-rwxr-xr-x root/root 44147 2017-07-28 19:32 ./usr/share/augustus/scripts/autoAugTrain.pl
-rw-r--r-- root/root 195 2017-07-28 19:32 ./usr/share/augustus/scripts/autoRun.pathInfo
-rwxr-xr-x root/root 3370 2017-07-28 19:32 ./usr/share/augustus/scripts/bedgraph2wig.pl
-rwxr-xr-x root/root 4442 2017-07-28 19:32 ./usr/share/augustus/scripts/blat2gbrowse.pl
-rwxr-xr-x root/root 30278 2017-07-28 19:32 ./usr/share/augustus/scripts/blat2hints.pl
-rwxr-xr-x root/root 11310 2017-07-28 19:32 ./usr/share/augustus/scripts/block2prfl.pl
-rwxr-xr-x root/root 2233 2017-07-28 19:32 ./usr/share/augustus/scripts/cegma2gff.pl
-rwxr-xr-x root/root 3843 2017-07-28 19:32 ./usr/share/augustus/scripts/checkParamArchive.pl
-rwxr-xr-x root/root 1151 2017-07-28 19:32 ./usr/share/augustus/scripts/checkUTR
-rwxr-xr-x root/root 535 2017-07-28 19:32 ./usr/share/augustus/scripts/cleanDOSfasta.pl
-rwxr-xr-x root/root 7558 2017-07-28 19:32 ./usr/share/augustus/scripts/clusterAndSplitGenes.pl
-rwxr-xr-x root/root 4879 2017-07-28 19:32 ./usr/share/augustus/scripts/createAugustusJoblist.pl
-rwxr-xr-x root/root 3233 2017-07-28 19:32 ./usr/share/augustus/scripts/del_from_prfl.pl
-rwxr-xr-x root/root 9675 2017-07-28 19:32 ./usr/share/augustus/scripts/evalCGP.pl
-rwxr-xr-x root/root 13247 2017-07-28 19:32 ./usr/share/augustus/scripts/eval_dualdecomp.pl
-rwxr-xr-x root/root 3043 2017-07-28 19:32 ./usr/share/augustus/scripts/exonerate2hints.pl
-rwxr-xr-x root/root 1301 2017-07-28 19:32 ./usr/share/augustus/scripts/exoniphyDb2hints.pl
-rwxr-xr-x root/root 507 2017-07-28 19:32 ./usr/share/augustus/scripts/extractTranscriptEnds.pl
-rwxr-xr-x root/root 435 2017-07-28 19:32 ./usr/share/augustus/scripts/filter-ppx.pl
-rwxr-xr-x root/root 850 2017-07-28 19:32 ./usr/share/augustus/scripts/filterGenes.pl
-rwxr-xr-x root/root 2188 2017-07-28 19:32 ./usr/share/augustus/scripts/filterGenesIn_mRNAname.pl
-rwxr-xr-x root/root 1716 2017-07-28 19:32 ./usr/share/augustus/scripts/filterGenesOut_mRNAname.pl
-rwxr-xr-x root/root 1122 2017-07-28 19:32 ./usr/share/augustus/scripts/filterInFrameStopCodons.pl
-rwxr-xr-x root/root 2923 2017-07-28 19:32 ./usr/share/augustus/scripts/filterMaf.pl
-rwxr-xr-x root/root 17619 2017-07-28 19:32 ./usr/share/augustus/scripts/filterPSL.pl
-rwxr-xr-x root/root 4465 2017-07-28 19:32 ./usr/share/augustus/scripts/filterShrimp.pl
-rwxr-xr-x root/root 2081 2017-07-28 19:32 ./usr/share/augustus/scripts/filterSpliceHints.pl
-rwxr-xr-x root/root 3098 2017-07-28 19:32 ./usr/share/augustus/scripts/gbSmallDNA2gff.pl
-rw-r--r-- root/root 8078 2017-07-28 19:32 ./usr/share/augustus/scripts/gbrowse.conf
-rwxr-xr-x root/root 3769 2017-07-28 19:32 ./usr/share/augustus/scripts/gbrowseold2gff3.pl
-rwxr-xr-x root/root 7331 2017-07-28 19:32 ./usr/share/augustus/scripts/getAnnoFasta.pl
-rwxr-xr-x root/root 17634 2017-07-28 19:32 ./usr/share/augustus/scripts/gff2gbSmallDNA.pl
-rw-r--r-- root/root 1758 2017-07-28 19:32 ./usr/share/augustus/scripts/gff2ps_mycustom
-rwxr-xr-x root/root 4074 2017-07-28 19:32 ./usr/share/augustus/scripts/gffGetmRNA.pl
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-rw-r--r-- root/root 8166 2017-07-28 19:32 ./usr/share/augustus/scripts/helpMod.pm
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-rw-r--r-- root/root 2706 2017-07-28 19:32 ./usr/share/augustus/scripts/webserver-results.body
-rw-r--r-- root/root 2134 2017-07-28 19:32 ./usr/share/augustus/scripts/webserver-results.head
-rw-r--r-- root/root 3105 2017-07-28 19:32 ./usr/share/augustus/scripts/webserver-results.tail
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drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/doc/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/doc/augustus/
lrwxrwxrwx root/root 0 2017-07-28 19:32 ./usr/share/doc/augustus/HISTORY.TXT.gz -> changelog.gz
-rw-r--r-- root/root 223 2017-07-28 19:32 ./usr/share/doc/augustus/changelog.Debian.armhf.gz
-rw-r--r-- root/root 826 2017-07-28 19:32 ./usr/share/doc/augustus/changelog.Debian.gz
-rw-r--r-- root/root 7497 2017-07-11 13:00 ./usr/share/doc/augustus/changelog.gz
-rw-r--r-- root/root 3495 2017-07-28 19:05 ./usr/share/doc/augustus/copyright
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/man/
drwxr-xr-x root/root 0 2017-07-28 19:32 ./usr/share/man/man1/
-rw-r--r-- root/root 565 2017-07-28 19:32 ./usr/share/man/man1/aln2wig.1.gz
-rw-r--r-- root/root 1665 2017-07-28 19:32 ./usr/share/man/man1/augustus.1.gz
-rw-r--r-- root/root 1499 2017-07-28 19:32 ./usr/share/man/man1/bam2hints.1.gz
-rw-r--r-- root/root 683 2017-07-28 19:32 ./usr/share/man/man1/bam2wig.1.gz
-rw-r--r-- root/root 579 2017-07-28 19:32 ./usr/share/man/man1/checkTargetSortedness.1.gz
-rw-r--r-- root/root 803 2017-07-28 19:32 ./usr/share/man/man1/compileSpliceCands.1.gz
-rw-r--r-- root/root 683 2017-07-28 19:32 ./usr/share/man/man1/etraining.1.gz
-rw-r--r-- root/root 1322 2017-07-28 19:32 ./usr/share/man/man1/fastBlockSearch.1.gz
-rw-r--r-- root/root 1719 2017-07-28 19:32 ./usr/share/man/man1/filterBam.1.gz
-rw-r--r-- root/root 1482 2017-07-28 19:32 ./usr/share/man/man1/homGeneMapping.1.gz
-rw-r--r-- root/root 2010 2017-07-28 19:32 ./usr/share/man/man1/joingenes.1.gz
-rw-r--r-- root/root 652 2017-07-28 19:32 ./usr/share/man/man1/prepareAlign.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 696792
Build-Time: 831
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 636
Job: augustus_3.3+dfsg-2
Machine Architecture: armhf
Package: augustus
Package-Time: 1551
Source-Version: 3.3+dfsg-2
Space: 696792
Status: successful
Version: 3.3+dfsg-2+b1
--------------------------------------------------------------------------------
Finished at 2018-04-10T23:01:03Z
Build needed 00:25:51, 696792k disc space