augustus →
3.3.1+dfsg-1 →
armhf → 2018-05-18 04:49:17
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| augustus 3.3.1+dfsg-1 (armhf) Fri, 18 May 2018 04:40:01 +0000 |
+==============================================================================+
Package: augustus
Version: 3.3.1+dfsg-1
Source Version: 3.3.1+dfsg-1
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-4c1bf62b-978b-4182-aa56-ad5024e2f812' 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 [12.5 MB]
Fetched 23.3 MB in 12s (1949 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://salsa.debian.org/med-team/augustus.git
Please use:
git clone https://salsa.debian.org/med-team/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 64.3 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main augustus 3.3.1+dfsg-1 (dsc) [1954 B]
Get:2 http://172.17.0.1/private buster-staging/main augustus 3.3.1+dfsg-1 (tar) [64.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main augustus 3.3.1+dfsg-1 (diff) [15.6 kB]
Fetched 64.3 MB in 25s (2572 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-VmB98w/augustus-3.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-VmB98w' 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-nJzgVR/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-nJzgVR/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-nJzgVR/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-nJzgVR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (11.8 kB/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 libsasl2-modules 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 40 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 15689 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, asciidoctor
Filtered Build-Depends: debhelper (>= 11), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-nJzgVR/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-nJzgVR/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ Sources [562 B]
Get:5 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ Packages [645 B]
Fetched 2540 B in 0s (14.1 kB/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 libsasl2-modules 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 libbz2-dev 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 libncurses-dev libncurses5-dev
libncurses6 libncursesw6 libnghttp2-14 libpipeline1 libpsl5 librbio2
librtmp1 libruby2.5 libsigsegv2 libspqr2 libsqlite3-dev libssh2-1
libsuitesparse-dev libsuitesparseconfig5 libtimedate-perl libtinfo6 libtool
libumfpack5 libxml2 libyaml-0-2 lzma-dev m4 man-db po-debconf rake ruby
ruby-asciidoctor ruby-did-you-mean ruby-minitest ruby-net-telnet
ruby-power-assert ruby-test-unit ruby2.5 rubygems-integration zlib1g
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 bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 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 libbz2-dev 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 libncurses-dev libncurses5-dev
libncurses6 libncursesw6 libnghttp2-14 libpipeline1 libpsl5 librbio2
librtmp1 libruby2.5 libsigsegv2 libspqr2 libsqlite3-dev libssh2-1
libsuitesparse-dev libsuitesparseconfig5 libtimedate-perl libtinfo6 libtool
libumfpack5 libxml2 libyaml-0-2 lzma-dev m4 man-db po-debconf rake ruby
ruby-asciidoctor 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:
zlib1g
1 upgraded, 101 newly installed, 0 to remove and 39 not upgraded.
Need to get 32.7 MB/58.2 MB of archives.
After this operation, 327 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-nJzgVR/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [928 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 zlib1g armhf 1:1.2.11.dfsg-1 [87.3 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.3-2 [1146 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.33-2 [234 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.33-2 [106 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.33-2 [64.7 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-6 [117 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf rubygems-integration all 1.11 [4994 B]
Get:12 http://172.17.0.1/private buster-staging/main armhf rake all 12.3.1-3 [66.9 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf ruby-did-you-mean all 1.2.1-1 [14.4 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf ruby-minitest all 5.10.3-1 [53.5 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf ruby-power-assert all 0.3.0-1 [7902 B]
Get:17 http://172.17.0.1/private buster-staging/main armhf ruby-test-unit all 3.2.7-1 [72.3 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libyaml-0-2 armhf 0.1.7-2 [39.9 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libruby2.5 armhf 2.5.1-1 [3125 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf ruby2.5 armhf 2.5.1-1 [384 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf ruby armhf 1:2.5.1 [11.3 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf ruby-asciidoctor all 1.5.6.2-2 [170 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf asciidoctor armhf 1.5.6.2-2 [43.0 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-3.1 [736 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-6 [434 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2.1 [547 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 17 [16.5 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.60-1 [95.6 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.041-1 [19.9 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.041-1 [12.0 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.56.1-2 [2754 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-6 [1218 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf debhelper all 11.2.1 [1013 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libsuitesparseconfig5 armhf 1:5.2.0+dfsg-1 [20.2 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf libamd2 armhf 1:5.2.0+dfsg-1 [26.5 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-3 [128 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-3 [21.8 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-12 [191 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.8.0-1 [103 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.8.0-1 [111 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-5+b2 [7004 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-5+b2 [232 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-5+b2 [325 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-5+b2 [49.3 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-5+b2 [58.5 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b8 [3694 B]
Get:55 http://172.17.0.1/private buster-staging/main armhf libbtf1 armhf 1:5.2.0+dfsg-1 [20.5 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf libbz2-dev armhf 1.0.6-8.1 [26.9 kB]
Get:57 http://172.17.0.1/private buster-staging/main armhf libcamd2 armhf 1:5.2.0+dfsg-1 [27.1 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libccolamd2 armhf 1:5.2.0+dfsg-1 [27.8 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libcolamd2 armhf 1:5.2.0+dfsg-1 [24.8 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.8.0-1 [1518 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libmetis5 armhf 5.1.0.dfsg-5 [131 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf libcholmod3 armhf 1:5.2.0+dfsg-1 [206 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.31.1-1 [69.4 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.20.1-1 [51.4 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libcxsparse3 armhf 1:5.2.0+dfsg-1 [48.6 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libgraphblas2 armhf 1:5.2.0+dfsg-1 [383 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.4+dfsg-6 [75.1 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.4+dfsg-6 [681 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.4+dfsg-6 [863 kB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.7-2 [259 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.7-2 [329 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libklu1 armhf 1:5.2.0+dfsg-1 [48.2 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.8.0-1 [1577 kB]
Get:74 http://172.17.0.1/private buster-staging/main armhf libldl2 armhf 1:5.2.0+dfsg-1 [20.4 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libumfpack5 armhf 1:5.2.0+dfsg-1 [125 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf librbio2 armhf 1:5.2.0+dfsg-1 [29.1 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libspqr2 armhf 1:5.2.0+dfsg-1 [64.7 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf libsuitesparse-dev armhf 1:5.2.0+dfsg-1 [895 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf liblpsolve55-dev armhf 5.5.0.15-4 [350 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libtinfo6 armhf 6.1+20180210-3 [307 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libncurses6 armhf 6.1+20180210-3 [78.3 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libncursesw6 armhf 6.1+20180210-3 [103 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf libncurses-dev armhf 6.1+20180210-3 [278 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.1+20180210-3 [924 B]
Get:85 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.23.1-1 [646 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf lzma-dev all 9.22-2.1 [44.7 kB]
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Setting up libboost-iostreams1.62.0:armhf (1.62.0+dfsg-5+b2) ...
Setting up ruby-did-you-mean (1.2.1-1) ...
Setting up libyaml-0-2:armhf (0.1.7-2) ...
Setting up libblas3:armhf (3.8.0-1) ...
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) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsuitesparseconfig5:armhf (1:5.2.0+dfsg-1) ...
Setting up libmetis5:armhf (5.1.0.dfsg-5) ...
Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-3) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up libcolamd2:armhf (1:5.2.0+dfsg-1) ...
Setting up rubygems-integration (1.11) ...
Setting up libccolamd2:armhf (1:5.2.0+dfsg-1) ...
Setting up icu-devtools (57.1-9) ...
Setting up liblzma-dev:armhf (5.2.2-1.3) ...
Setting up libkeyutils1:armhf (1.5.9-9.2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up ruby-minitest (5.10.3-1) ...
Setting up libgslcblas0:armhf (2.4+dfsg-6) ...
Setting up libncurses6:armhf (6.1+20180210-3) ...
Setting up autopoint (0.19.8.1-6) ...
Setting up ruby-power-assert (0.3.0-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-1) ...
Setting up libfile-stripnondeterminism-perl (0.041-1) ...
Setting up libbtf1:armhf (1:5.2.0+dfsg-1) ...
Setting up libldl2:armhf (1:5.2.0+dfsg-1) ...
Setting up libcxsparse3:armhf (1:5.2.0+dfsg-1) ...
Setting up lzma-dev (9.22-2.1) ...
Setting up ruby-test-unit (3.2.7-1) ...
Setting up libgsl23:armhf (2.4+dfsg-6) ...
Setting up gettext (0.19.8.1-6) ...
Setting up libblas-dev:armhf (3.8.0-1) ...
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) ...
Setting up liblapack3:armhf (3.8.0-1) ...
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 libncursesw6:armhf (6.1+20180210-3) ...
Setting up librbio2:armhf (1:5.2.0+dfsg-1) ...
Setting up libboost-regex1.62.0:armhf (1.62.0+dfsg-5+b2) ...
Setting up libcamd2:armhf (1:5.2.0+dfsg-1) ...
Setting up libbamtools-dev:armhf (2.5.1+dfsg-3) ...
Setting up autoconf (2.69-11) ...
Setting up libicu-dev (57.1-9) ...
Setting up file (1:5.33-2) ...
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 (1:1.15.1-3.1) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libncurses-dev:armhf (6.1+20180210-3) ...
Setting up liblapack-dev:armhf (3.8.0-1) ...
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 (2.4.6-2.1) ...
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+b2) ...
Setting up libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-5+b2) ...
Setting up libklu1:armhf (1:5.2.0+dfsg-1) ...
Setting up libcholmod3:armhf (1:5.2.0+dfsg-1) ...
Setting up libncurses5-dev:armhf (6.1+20180210-3) ...
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 rake (12.3.1-3) ...
Setting up dh-strip-nondeterminism (0.041-1) ...
Setting up debhelper (11.2.1) ...
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 ruby-asciidoctor (1.5.6.2-2) ...
Setting up asciidoctor (1.5.6.2-2) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.27-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.30-15+rpi1 dpkg-dev_1.19.0.5 g++-7_7.3.0-12 gcc-7_7.3.0-12 libc6-dev_2.27-3+rpi1 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 linux-libc-dev_4.15.17-1+rpi1
Package versions: adduser_3.117 apt_1.6.1 asciidoctor_1.5.6.2-2 autoconf_2.69-11 automake_1:1.15.1-3.1 autopoint_0.19.8.1-6 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_4.4.18-2+b1 binutils_2.30-15+rpi1 binutils-arm-linux-gnueabihf_2.30-15+rpi1 binutils-common_2.30-15+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.31.1-0.5 build-essential_12.4+b1 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_11.2.1 debianutils_4.8.4 dh-autoreconf_17 dh-strip-nondeterminism_0.041-1 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_1.44.1-2 e2fsprogs_1.44.1-2 e2fsprogs-l10n_1.44.1-2 fakeroot_1.22-2 fdisk_2.31.1-0.5 file_1:5.33-2 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-7_7.3.0-12 gcc-7-base_7.3.0-12 gcc-8-base_8-20180414-1+rpi1 gettext_0.19.8.1-6 gettext-base_0.19.8.1-6 gnupg_2.2.5-1 gnupg-agent_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_1.6.1 libarchive-zip-perl_1.60-1 libargon2-0_0~20161029-2 libasan4_7.3.0-12 libassuan0_2.5.1-2 libatomic1_8-20180414-1+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_2.30-15+rpi1 libblas-dev_3.8.0-1 libblas3_3.8.0-1 libblkid1_2.31.1-0.5 libboost-iostreams-dev_1.62.0.1+b8 libboost-iostreams1.62-dev_1.62.0+dfsg-5+b2 libboost-iostreams1.62.0_1.62.0+dfsg-5+b2 libboost-regex1.62-dev_1.62.0+dfsg-5+b2 libboost-regex1.62.0_1.62.0+dfsg-5+b2 libboost1.62-dev_1.62.0+dfsg-5+b2 libbsd0_0.8.7-1 libbtf1_1:5.2.0+dfsg-1 libbz2-1.0_1.0.6-8.1 libbz2-dev_1.0.6-8.1 libc-bin_2.27-3+rpi1 libc-dev-bin_2.27-3+rpi1 libc6_2.27-3+rpi1 libc6-dev_2.27-3+rpi1 libcamd2_1:5.2.0+dfsg-1 libcap-ng0_0.7.7-3.1+b1 libcap2_1:2.25-1.2 libcc1-0_8-20180414-1+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_1.44.1-2 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_1.44.1-2 libfakeroot_1.22-2 libfdisk1_2.31.1-0.5 libffi6_3.2.1-8 libfile-stripnondeterminism-perl_0.041-1 libgcc-7-dev_7.3.0-12 libgcc1_1:8-20180414-1+rpi1 libgcrypt20_1.8.2-2 libgdbm-compat4_1.14.1-6 libgdbm3_1.8.3-14 libgdbm5_1.14.1-6 libgfortran4_7.3.0-12 libglib2.0-0_2.56.1-2 libgmp10_2:6.1.2+dfsg-3 libgnutls30_3.5.18-1 libgomp1_8-20180414-1+rpi1 libgpg-error0_1.29-4 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_1.33-2.2 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_3.8.0-1 liblapack3_3.8.0-1 libldap-2.4-2_2.4.45+dfsg-1 libldap-common_2.4.45+dfsg-1 libldl2_1:5.2.0+dfsg-1 liblpsolve55-dev_5.5.0.15-4 liblz4-1_1.8.1.2-1+rpi1 liblzma-dev_5.2.2-1.3 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.33-2 libmagic1_1:5.33-2 libmetis5_5.1.0.dfsg-5 libmount1_2.31.1-0.5 libmpc3_1.1.0-1 libmpfr6_4.0.1-1 libncurses-dev_6.1+20180210-3 libncurses5_6.1-1 libncurses5-dev_6.1+20180210-3 libncurses6_6.1+20180210-3 libncursesw5_6.1-1 libncursesw6_6.1+20180210-3 libnettle6_3.4-1 libnghttp2-14_1.31.1-1 libnpth0_1.5-3 libnss-systemd_238-4 libp11-kit0_0.23.10-2 libpam-modules_1.1.8-3.7 libpam-modules-bin_1.1.8-3.7 libpam-runtime_1.1.8-3.7 libpam-systemd_238-4 libpam0g_1.1.8-3.7 libpcre3_2:8.39-9 libperl5.24_5.24.1-7 libperl5.26_5.26.2-2 libpipeline1_1.5.0-1 libplymouth4_0.9.3-2 libpng16-16_1.6.34-1 libprocps6_2:3.3.14-1 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-3.1 libsasl2-modules_2.1.27~101-g0780600+dfsg-3.1 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3.1 libseccomp2_2.3.3-1 libselinux1_2.7-2 libsemanage-common_2.7-2 libsemanage1_2.7-2 libsepol1_2.7-1 libsigsegv2_2.12-2 libsmartcols1_2.31.1-0.5 libspqr2_1:5.2.0+dfsg-1 libsqlite3-0_3.23.1-1 libsqlite3-dev_3.23.1-1 libss2_1.44.1-2 libssh2-1_1.8.0-1 libssl1.1_1.1.0h-2 libstdc++-7-dev_7.3.0-12 libstdc++6_8-20180414-1+rpi1 libsuitesparse-dev_1:5.2.0+dfsg-1 libsuitesparseconfig5_1:5.2.0+dfsg-1 libsystemd0_238-4 libtasn1-6_4.13-2 libtimedate-perl_2.3000-2 libtinfo5_6.1-1 libtinfo6_6.1+20180210-3 libtool_2.4.6-2.1 libubsan0_7.3.0-12 libudev1_238-4 libumfpack5_1:5.2.0+dfsg-1 libunistring2_0.9.8-1 libustr-1.0-1_1.0.4-6 libuuid1_2.31.1-0.5 libxml2_2.9.4+dfsg1-6.1 libyaml-0-2_0.1.7-2 libzstd1_1.3.3+dfsg-2+rpi1 linux-base_4.5 linux-libc-dev_4.15.17-1+rpi1 login_1:4.5-1 lsb-base_9.20170808+rpi1 lzma-dev_9.22-2.1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.8.3-2 mawk_1.3.3-17 mount_2.31.1-0.5 multiarch-support_2.27-3+rpi1 nano_2.9.5-1 ncurses-base_6.1-1 ncurses-bin_6.1-1 netbase_5.4 openssl_1.1.0h-2 passwd_1:4.5-1 patch_2.7.6-2 perl_5.26.2-2 perl-base_5.26.2-2 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.2-3 pinentry-curses_1.1.0-1 plymouth_0.9.3-2 po-debconf_1.0.20 procps_2:3.3.14-1 rake_12.3.1-3 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 ruby_1:2.5.1 ruby-asciidoctor_1.5.6.2-2 ruby-did-you-mean_1.2.1-1 ruby-minitest_5.10.3-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.3.0-1 ruby-test-unit_3.2.7-1 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_238-4 systemd-sysv_238-4 sysvinit-utils_2.88dsf-59.10 tar_1.29b-2 tzdata_2018d-1 udev_238-4 util-linux_2.31.1-0.5 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Tue May 15 22:38:01 2018 UTC
gpgv: using RSA key 8451F9178172E7E2DC73F79551F84A8FECCA7E09
gpgv: issuer "satta@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./augustus_3.3.1+dfsg-1.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.3.1+dfsg
dpkg-source: info: unpacking augustus_3.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.3.1+dfsg-1.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 disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-4c1bf62b-978b-4182-aa56-ad5024e2f812
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.3.1+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build augustus-3.3.1+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
(cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
/bin/sh: 1: cd: can't cd to ../../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
rm -rf *o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
rm -f bam2wig bam2wig.o
rm -f ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness'
rm -f *.o checkTargetSortedness
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o
rm -f ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
rm -rf bin
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/aln2wig'
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
g++ -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+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-3.3.1+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/bcftools/ -I/usr/include/tabix/ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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
cc -Wall -O2 -I/usr/include/samtools/ -I. -I/usr/include/htslib/ -I/usr/include/bcftools/ -I/usr/include/tabix/ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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 -lbz2 -llzma
cp bam2wig ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/checkTargetSortedness'
cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+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-3.3.1+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+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-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now;
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping/src'
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+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-3.3.1+dfsg/auxprogs/joingenes'
dh_auto_build
make -j4 -Oline "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
mkdir -p bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {const PP::Column&}; _Tp = PP::Column; _Alloc = std::allocator<PP::Column>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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_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, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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
/usr/include/c++/7/bits/vector.tcc:394:7: 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
/usr/include/c++/7/bits/vector.tcc: In member function 'bool PP::Block::initThresholds()':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:712:18: 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:712:18: 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/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, _Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator<PP::Block>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void PP::Profile::parse_stream(std::istream&)':
/usr/include/c++/7/bits/vector.tcc:105:21: 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(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _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:2395:7: 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:712:18: 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:61:0,
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_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {const PP::BonusProbEntry&}; _Tp = PP::BonusProbEntry; _Alloc = std::allocator<PP::BonusProbEntry>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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/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);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
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 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [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:2130:5: 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: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SubstateId&>, std::tuple<>}; _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:2395:7: 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
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_map.h: In member function 'void ViterbiSubmapType::eraseAndDecCounts(ViterbiSubmapType::iterator) const':
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h: In member function 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)':
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
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 PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)':
/usr/include/c++/7/bits/stl_tree.h:1153:14: 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::postProcessing(const Double&)':
/usr/include/c++/7/bits/stl_tree.h:1153:14: 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);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
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_map.h: In member function 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)':
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h: In member function 'void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)':
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
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 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)':
/usr/include/c++/7/bits/stl_tree.h:1153:14: 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);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
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_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void StateModel::initPredecessors(Matrix<LLDouble>&, int)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include
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: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/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, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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/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: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 function 'void examineBaseCountOfGeneSeq(AnnoSequence*)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {const ViterbiSubmapType&}; _Tp = ViterbiSubmapType; _Alloc = std::allocator<ViterbiSubmapType>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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>::
^~~~~~~~~~~~~~~~~~~
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: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:1153:14: 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:1153:14: 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);
~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
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, _Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator<ViterbiEntryType>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/vector.tcc: In member function 'void ViterbiColumnType::addState(int, signed char)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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 '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 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [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:2130:5: 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: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SubstateId&>, std::tuple<>}; _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:2395:7: 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>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/map:61:0,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/7/bits/stl_map.h: In member function 'void ViterbiSubmapType::registerPredecessors()':
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
/usr/include/c++/7/bits/stl_map.h:493:4: 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
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
^~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include
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 member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity<Feature>; _Compare = std::less<Feature>; _Alloc = std::allocator<Feature>]':
/usr/include/c++/7/bits/stl_tree.h:2130:5: 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/set:61:0,
from ../include/extrinsicinfo.hh:28,
from extrinsicinfo.cc:31:
/usr/include/c++/7/bits/stl_set.h: In constructor 'std::set<_Key, _Compare, _Alloc>::set(_InputIterator, _InputIterator) [with _InputIterator = std::_List_iterator<Feature>; _Key = Feature; _Compare = std::less<Feature>; _Alloc = std::allocator<Feature>]':
/usr/include/c++/7/bits/stl_set.h:181:2: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set(_InputIterator __first, _InputIterator __last)
^~~
/usr/include/c++/7/bits/stl_set.h:181:2: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
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
extrinsicinfo.cc: In member function 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)':
extrinsicinfo.cc:2532:54: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set <Feature> startHS(flist.begin(), flist.end());
^
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
extrinsicinfo.cc:2573:53: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set <Feature> stopHS(flist.begin(), flist.end());
^
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
extrinsicinfo.cc:2611:52: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set <Feature> dssHS(flist.begin(), flist.end());
^
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
extrinsicinfo.cc:2657:52: note: parameter passing for argument of type 'std::_List_iterator<Feature>' changed in GCC 7.1
set <Feature> assHS(flist.begin(), flist.end());
^
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
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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 constructor 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:105:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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/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::onlineLargeMarginTraining(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)':
/usr/include/c++/7/bits/stl_vector.h:712:18: 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-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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:712:18: 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-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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: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-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" > cxxflags
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/7/bits/vector.tcc:394:7: 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::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);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
cp prepareAlign ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
cp augustus ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
cp fastBlockSearch ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
cp etraining ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2hints'
make[4]: 'bam2hints' is up to date.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/compileSpliceCands'
make[4]: 'compileSpliceCands' is up to date.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+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
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
filterBam compiled with BAMTOOLS=/usr/include/bamtools
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
mv filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/filterBam'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
(cd src; make)
make[5]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/homGeneMapping'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/joingenes'
make[4]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
cd bam2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/bam2wig'
make[4]: 'bam2wig' is up to date.
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
cd utrrnaseq/Debug; make all;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building file: ../src/Compute_UTRs.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Compiler
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp"
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building: ../src/Compute_UTRs.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building file: ../src/Coord_Transform.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Compiler
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp"
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building: ../src/Coord_Transform.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building file: ../src/Genomic_Data.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Compiler
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp"
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building: ../src/Genomic_Data.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building file: ../src/Splice_Sites.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Compiler
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp"
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building: ../src/Splice_Sites.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building file: ../src/Supporting_Methods.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Compiler
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp"
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building: ../src/Supporting_Methods.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building file: ../src/Test.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Compiler
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp"
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building: ../src/Test.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building file: ../src/UTRs.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Compiler
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp"
../src/UTRs.cpp: In static member function 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map<unsigned int, double>&)':
../src/UTRs.cpp:355:64: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
vector<double>::iterator jt = min_element(d.begin(), d.end());
^
In file included from /usr/include/c++/7/bits/stl_algobase.h:71:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/7/bits/predefined_ops.h: In member function 'constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Iterator2 = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]':
/usr/include/c++/7/bits/predefined_ops.h:42:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
operator()(_Iterator1 __it1, _Iterator2 __it2) const
^~~~~~~~
/usr/include/c++/7/bits/predefined_ops.h:42:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/7/algorithm:62:0,
from /usr/include/boost/core/swap.hpp:25,
from /usr/include/boost/utility/swap.hpp:15,
from /usr/include/boost/tuple/detail/tuple_basic.hpp:40,
from /usr/include/boost/tuple/tuple.hpp:28,
from ../src/Compute_UTRs.hpp:16,
from ../src/UTRs.cpp:9:
/usr/include/c++/7/bits/stl_algo.h: In function 'constexpr _ForwardIterator std::__min_element(_ForwardIterator, _ForwardIterator, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/7/bits/stl_algo.h:5582:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
__min_element(_ForwardIterator __first, _ForwardIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:5582:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5589:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
if (__comp(__first, __result))
~~~~~~^~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h: In function 'constexpr _FIter std::min_element(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]':
/usr/include/c++/7/bits/stl_algo.h:5604:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
inline min_element(_ForwardIterator __first, _ForwardIterator __last)
^~~~~~~~~~~
/usr/include/c++/7/bits/stl_algo.h:5604:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/7/bits/stl_algo.h:5614:41: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
In file included from /usr/include/c++/7/vector:64:0,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/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, std::allocator<double> > >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:69:0,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/7/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/7/bits/vector.tcc:394:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >}' changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/vector:63:0,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator<double>]':
/usr/include/c++/7/bits/stl_uninitialized.h:312:69: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
^
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:289:63: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
{ return std::uninitialized_copy(__first, __last, __result); }
^
/usr/include/c++/7/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
uninitialized_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:134:41: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninit_copy(__first, __last, __result);
^
/usr/include/c++/7/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__uninit_copy(_InputIterator __first, _InputIterator __last,
^~~~~~~~~~~~~
/usr/include/c++/7/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/7/bits/stl_uninitialized.h:101:53: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
{ return std::copy(__first, __last, __result); }
^
In file included from /usr/include/c++/7/bits/char_traits.h:39:0,
from /usr/include/c++/7/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/7/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
copy(_II __first, _II __last, _OI __result)
^~~~
/usr/include/c++/7/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/7/bits/stl_algobase.h:67:0,
from /usr/include/c++/7/bits/char_traits.h:39,
from /usr/include/c++/7/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/7/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/7/bits/stl_iterator.h:1241:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
__miter_base(move_iterator<_Iterator> __it)
^~~~~~~~~~~~
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building: ../src/UTRs.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building file: ../src/main.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Compiler
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp"
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building: ../src/main.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Building target: utrrnaseq
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Invoking: GCC C++ Linker
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
Finished building target: utrrnaseq
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
cp utrrnaseq ../../../bin/utrrnaseq
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs/utrrnaseq/Debug'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg/auxprogs'
asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+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-3.3.1+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_installchangelogs -k HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.1+dfsg'
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/augustus/usr/bin/utrrnaseq 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/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/bam2hints 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/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/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/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/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/augustus 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/bam2wig was not linked against libbz2.so.1.0 (it uses 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 liblzma.so.5 (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.6 (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 libtinfo.so.6 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.3.1+dfsg-1_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.3.1+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../augustus_3.3.1+dfsg-1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build augustus-3.3.1+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2018-05-18T04:49:12Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.3.1+dfsg-1_armhf.changes:
------------------------------------
Format: 1.8
Date: Sat, 12 May 2018 08:25:35 +0200
Source: augustus
Binary: augustus augustus-data augustus-doc
Architecture: armhf
Version: 3.3.1+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
augustus-data - data files for AUGUSTUS
augustus-doc - documentation files for AUGUSTUS
Changes:
augustus (3.3.1+dfsg-1) unstable; urgency=medium
.
[ Steffen Moeller ]
* debian/upstream/metadata: RRID -> SciCrunch
.
[ Sascha Steinbiss ]
* New upstream release.
* Fix typo in manpage.
* Remove obsolete Testsuite entry.
* Bump Standards-Version.
* Remove old patches.
* Update VCS-* links.
* Bump debhelper requirement to version 11.
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a32da59d0e30bc7194fa7cdc9c4a614c3f09af4f683a8c1021d59a6ab7153fdd 7200 augustus_3.3.1+dfsg-1_armhf.buildinfo
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Files:
d72ecdf9ce2d97055232acb012a4a76a 16486476 debug optional augustus-dbgsym_3.3.1+dfsg-1_armhf.deb
383e550760550b9820188b2b814ef110 7200 science optional augustus_3.3.1+dfsg-1_armhf.buildinfo
f9bab9bef6f6b196a23bbadfce27e74c 928088 science optional augustus_3.3.1+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.3.1+dfsg-1_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 16486476 bytes: control archive=1172 bytes.
920 bytes, 13 lines control
1378 bytes, 13 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.3.1+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 16921
Depends: augustus (= 3.3.1+dfsg-1)
Built-Using: samtools-legacy (= 0.1.19-2)
Section: debug
Priority: optional
Description: debug symbols for augustus
Build-Ids: 08287bcaf0b251c2df41dcab265b64fb43c1aa56 2a9e0ffa3ae3359d983632019ed5a090eedab707 2e27bcc5bf5cec6919e20552d435c0ab1d28f4e0 3492b1adb213bc78f286fd4f29bdb74b6e0c4260 40fb83c4b1a54e6db1dabd621ebc62927d51a992 41debf173bcb2b8efc4da5fcc82d7e5a0726991d 4c7e4145e0a44d35e8c96481821c6b6bbc1e9c7d 5cd0fafe1222b3d555d752cd560952423a6aacaf a1418122ae30a854fc3bb0f2a75f851ed0607bc0 c9fdbee678ce05a7a2dd33a3a3c0db5c91fb587e cc9ae2f06807eb34c3374dc6bbba0e2231c49a1a d30fd45b27fa8af18f610204245640e56a55b131 da06fb48c97ca82d4b71961f0cc2073e3ad5f942
drwxr-xr-x root/root 0 2018-05-12 06:25 ./
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/08/
-rw-r--r-- root/root 18528 2018-05-12 06:25 ./usr/lib/debug/.build-id/08/287bcaf0b251c2df41dcab265b64fb43c1aa56.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/2a/
-rw-r--r-- root/root 597260 2018-05-12 06:25 ./usr/lib/debug/.build-id/2a/9e0ffa3ae3359d983632019ed5a090eedab707.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/2e/
-rw-r--r-- root/root 13208 2018-05-12 06:25 ./usr/lib/debug/.build-id/2e/27bcc5bf5cec6919e20552d435c0ab1d28f4e0.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 140788 2018-05-12 06:25 ./usr/lib/debug/.build-id/34/92b1adb213bc78f286fd4f29bdb74b6e0c4260.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/40/
-rw-r--r-- root/root 6175328 2018-05-12 06:25 ./usr/lib/debug/.build-id/40/fb83c4b1a54e6db1dabd621ebc62927d51a992.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/41/
-rw-r--r-- root/root 977944 2018-05-12 06:25 ./usr/lib/debug/.build-id/41/debf173bcb2b8efc4da5fcc82d7e5a0726991d.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/4c/
-rw-r--r-- root/root 655732 2018-05-12 06:25 ./usr/lib/debug/.build-id/4c/7e4145e0a44d35e8c96481821c6b6bbc1e9c7d.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/5c/
-rw-r--r-- root/root 644408 2018-05-12 06:25 ./usr/lib/debug/.build-id/5c/d0fafe1222b3d555d752cd560952423a6aacaf.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/a1/
-rw-r--r-- root/root 6930772 2018-05-12 06:25 ./usr/lib/debug/.build-id/a1/418122ae30a854fc3bb0f2a75f851ed0607bc0.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/c9/
-rw-r--r-- root/root 989836 2018-05-12 06:25 ./usr/lib/debug/.build-id/c9/fdbee678ce05a7a2dd33a3a3c0db5c91fb587e.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/cc/
-rw-r--r-- root/root 22164 2018-05-12 06:25 ./usr/lib/debug/.build-id/cc/9ae2f06807eb34c3374dc6bbba0e2231c49a1a.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/d3/
-rw-r--r-- root/root 113464 2018-05-12 06:25 ./usr/lib/debug/.build-id/d3/0fd45b27fa8af18f610204245640e56a55b131.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/lib/debug/.build-id/da/
-rw-r--r-- root/root 18312 2018-05-12 06:25 ./usr/lib/debug/.build-id/da/06fb48c97ca82d4b71961f0cc2073e3ad5f942.debug
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/share/
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/share/doc/
lrwxrwxrwx root/root 0 2018-05-12 06:25 ./usr/share/doc/augustus-dbgsym -> augustus
augustus_3.3.1+dfsg-1_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 928088 bytes: control archive=4620 bytes.
1334 bytes, 22 lines control
9589 bytes, 128 lines md5sums
Package: augustus
Version: 3.3.1+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 4065
Depends: libbamtools2.5.1, libbz2-1.0, libc6 (>= 2.15), libgcc1 (>= 1:3.5), libhts2 (>= 1.0), liblzma5 (>= 5.1.1alpha+20110809), libncurses6 (>= 6), libstdc++6 (>= 6), libtinfo6 (>= 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 2018-05-12 06:25 ./
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/
drwxr-xr-x root/root 0 2018-05-12 06:25 ./usr/bin/
-rwxr-xr-x root/root 9684 2018-05-12 06:25 ./usr/bin/aln2wig
-rwxr-xr-x root/root 1057044 2018-05-12 06:25 ./usr/bin/augustus
-rwxr-xr-x root/root 26540 2018-05-12 06:25 ./usr/bin/bam2hints
-rwxr-xr-x root/root 96748 2018-05-12 06:25 ./usr/bin/bam2wig
-rwxr-xr-x root/root 88504 2018-05-12 06:25 ./usr/bin/checkTargetSortedness
-rwxr-xr-x root/root 13780 2018-05-12 06:25 ./usr/bin/compileSpliceCands
-rwxr-xr-x root/root 1204492 2018-05-12 06:25 ./usr/bin/etraining
-rwxr-xr-x root/root 216924 2018-05-12 06:25 ./usr/bin/fastBlockSearch
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
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Build Architecture: armhf
Build-Space: 863456
Build-Time: 249
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 247
Job: augustus_3.3.1+dfsg-1
Machine Architecture: armhf
Package: augustus
Package-Time: 551
Source-Version: 3.3.1+dfsg-1
Space: 863456
Status: successful
Version: 3.3.1+dfsg-1
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Finished at 2018-05-18T04:49:12Z
Build needed 00:09:11, 863456k disk space