augustus →
3.2.3+dfsg-1+b2 →
armhf → 2017-07-29 12:11:18
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| augustus 3.2.3+dfsg-1+b2 (armhf) Sat, 29 Jul 2017 11:43:00 +0000 |
+==============================================================================+
Package: augustus
Version: 3.2.3+dfsg-1+b2
Source Version: 3.2.3+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/buster-staging-armhf-sbuild-c0958a79-3130-4666-bc28-9ed28cf5528c' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Hit:1 http://172.17.0.1/private buster-staging InRelease
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'augustus' packaging is maintained in the 'Git' version control system at:
https://anonscm.debian.org/git/debian-med/augustus.git
Please use:
git clone https://anonscm.debian.org/git/debian-med/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 45.2 MB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main augustus 3.2.3+dfsg-1 (dsc) [2274 B]
Get:2 http://172.17.0.1/private buster-staging/main augustus 3.2.3+dfsg-1 (tar) [45.2 MB]
Get:3 http://172.17.0.1/private buster-staging/main augustus 3.2.3+dfsg-1 (diff) [16.0 kB]
Fetched 45.2 MB in 5s (8002 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-OTHmeC/augustus-3.2.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-OTHmeC' 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-8BuJ4Y/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-8BuJ4Y/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-8BuJ4Y/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Packages [429 B]
Fetched 2105 B in 0s (2863 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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 libssl1.1 openssl
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 1 not upgraded.
Need to get 776 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [776 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 776 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14837 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) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 10), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev, asciidoctor
Filtered Build-Depends: debhelper (>= 10), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libhts-dev, libncurses5-dev, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-8BuJ4Y/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-8BuJ4Y/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Sources [557 B]
Get:5 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Packages [638 B]
Fetched 2528 B in 0s (3438 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install augustus build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism file gettext gettext-base gfortran
gfortran-6 groff-base icu-devtools intltool-debian libamd2
libarchive-zip-perl libbam-dev libbamtools-dev libbamtools2.4.0
libblas-common libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex1.62-dev
libboost-regex1.62.0 libboost1.62-dev libbsd0 libbtf1 libcamd2 libccolamd2
libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcxsparse3
libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
libgsl-dev libgsl2 libgssapi-krb5-2 libhts-dev libhts2 libicu-dev libicu57
libk5crypto3 libkeyutils1 libklu1 libkrb5-3 libkrb5support0 liblapack-dev
liblapack3 libldap-2.4-2 libldap-common libldl2 liblpsolve55-dev
libmagic-mgc libmagic1 libmetis5 libncurses5-dev libnghttp2-14 libpipeline1
libpsl5 librbio2 librtmp1 libruby2.3 libsasl2-2 libsasl2-modules-db
libsigsegv2 libspqr2 libsqlite3-dev libssh2-1 libssl1.0.2 libsuitesparse-dev
libsuitesparseconfig4 libtimedate-perl libtinfo-dev libtool libumfpack5
libxml2 libyaml-0-2 m4 man-db po-debconf rake ruby ruby-did-you-mean
ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3
rubygems-integration zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
gfortran-6-doc libgfortran3-dbg libcoarrays-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 ncurses-doc sqlite3-doc libtool-doc gcj-jdk m4-doc less www-browser
libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx-cur libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs krb5-locales publicsuffix libsasl2-modules libltdl-dev
xml-core 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 gfortran
gfortran-6 groff-base icu-devtools intltool-debian libamd2
libarchive-zip-perl libbam-dev libbamtools-dev libbamtools2.4.0
libblas-common libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.62-dev libboost-iostreams1.62.0 libboost-regex1.62-dev
libboost-regex1.62.0 libboost1.62-dev libbsd0 libbtf1 libcamd2 libccolamd2
libcholmod3 libcolamd2 libcroco3 libcurl3-gnutls libcxsparse3
libfile-stripnondeterminism-perl libgfortran-6-dev libgfortran3 libglib2.0-0
libgsl-dev libgsl2 libgssapi-krb5-2 libhts-dev libhts2 libicu-dev libicu57
libk5crypto3 libkeyutils1 libklu1 libkrb5-3 libkrb5support0 liblapack-dev
liblapack3 libldap-2.4-2 libldap-common libldl2 liblpsolve55-dev
libmagic-mgc libmagic1 libmetis5 libncurses5-dev libnghttp2-14 libpipeline1
libpsl5 librbio2 librtmp1 libruby2.3 libsasl2-2 libsasl2-modules-db
libsigsegv2 libspqr2 libsqlite3-dev libssh2-1 libssl1.0.2 libsuitesparse-dev
libsuitesparseconfig4 libtimedate-perl libtinfo-dev libtool libumfpack5
libxml2 libyaml-0-2 m4 man-db po-debconf rake ruby ruby-did-you-mean
ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3
rubygems-integration sbuild-build-depends-augustus-dummy zlib1g-dev
0 upgraded, 101 newly installed, 0 to remove and 1 not upgraded.
Need to get 62.7 MB of archives.
After this operation, 334 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-8BuJ4Y/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [844 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.3-9 [1005 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.8.6-1 [95.7 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 9.0.12+nmu1 [178 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.4.2-1 [24.2 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.7.6.1-2 [1014 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf libssl1.0.2 armhf 1.0.2l-2 [893 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.30-1 [222 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.30-1 [105 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.30-1 [63.4 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-2+b1 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libkeyutils1 armhf 1.5.9-9 [11.9 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf libkrb5support0 armhf 1.15.1-2 [58.4 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf libk5crypto3 armhf 1.15.1-2 [115 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf libkrb5-3 armhf 1.15.1-2 [265 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf libgssapi-krb5-2 armhf 1.15.1-2 [132 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf libsasl2-modules-db armhf 2.1.27~101-g0780600+dfsg-3 [66.9 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libsasl2-2 armhf 2.1.27~101-g0780600+dfsg-3 [98.1 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf libldap-common all 2.4.44+dfsg-8 [85.3 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libldap-2.4-2 armhf 2.4.44+dfsg-8 [195 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libicu57 armhf 57.1-6 [7427 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-3 [601 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf rubygems-integration all 1.11 [4994 B]
Get:24 http://172.17.0.1/private buster-staging/main armhf rake all 12.0.0-1 [45.7 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf ruby-did-you-mean all 1.0.0-2 [11.2 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf ruby-minitest all 5.10.2-1 [52.2 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf ruby-power-assert all 0.3.0-1 [7902 B]
Get:29 http://172.17.0.1/private buster-staging/main armhf ruby-test-unit all 3.2.5-1 [71.7 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf libyaml-0-2 armhf 0.1.7-2 [39.9 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf libruby2.3 armhf 2.3.3-1 [2864 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf ruby2.3 armhf 2.3.3-1 [186 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf ruby armhf 1:2.3.3 [10.8 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf asciidoctor all 1.5.5-1 [183 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.11-1 [29.3 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-1 [185 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-10 [338 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20161112.1 [73.4 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.15.1-2 [736 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-2 [433 kB]
Get:41 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-2 [545 kB]
Get:42 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 14 [15.9 kB]
Get:43 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.59-1 [95.5 kB]
Get:44 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 0.038-1 [17.6 kB]
Get:45 http://172.17.0.1/private buster-staging/main armhf libtimedate-perl all 2.3000-2 [42.2 kB]
Get:46 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 0.038-1 [11.1 kB]
Get:47 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.52.3-1 [2576 kB]
Get:48 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-1 [132 kB]
Get:49 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-2+b1 [1220 kB]
Get:50 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.4 [26.3 kB]
Get:51 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.20 [247 kB]
Get:52 http://172.17.0.1/private buster-staging/main armhf debhelper all 10.6.4 [970 kB]
Get:53 http://172.17.0.1/private buster-staging/main armhf libgfortran3 armhf 6.4.0-1+rpi1 [166 kB]
Get:54 http://172.17.0.1/private buster-staging/main armhf libgfortran-6-dev armhf 6.4.0-1+rpi1 [199 kB]
Get:55 http://172.17.0.1/private buster-staging/main armhf gfortran-6 armhf 6.4.0-1+rpi1 [5420 kB]
Get:56 http://172.17.0.1/private buster-staging/main armhf gfortran armhf 4:6.3.0-4d1 [1358 B]
Get:57 http://172.17.0.1/private buster-staging/main armhf icu-devtools armhf 57.1-6 [156 kB]
Get:58 http://172.17.0.1/private buster-staging/main armhf libsuitesparseconfig4 armhf 1:4.5.5-1 [18.6 kB]
Get:59 http://172.17.0.1/private buster-staging/main armhf libamd2 armhf 1:4.5.5-1 [30.4 kB]
Get:60 http://172.17.0.1/private buster-staging/main armhf libbam-dev armhf 0.1.19-2 [109 kB]
Get:61 http://172.17.0.1/private buster-staging/main armhf libbamtools2.4.0 armhf 2.4.1+dfsg-1 [160 kB]
Get:62 http://172.17.0.1/private buster-staging/main armhf zlib1g-dev armhf 1:1.2.8.dfsg-5 [198 kB]
Get:63 http://172.17.0.1/private buster-staging/main armhf libbamtools-dev armhf 2.4.1+dfsg-1 [213 kB]
Get:64 http://172.17.0.1/private buster-staging/main armhf libblas-common armhf 3.7.1-1 [14.6 kB]
Get:65 http://172.17.0.1/private buster-staging/main armhf libblas3 armhf 3.7.1-1 [108 kB]
Get:66 http://172.17.0.1/private buster-staging/main armhf libblas-dev armhf 3.7.1-1 [118 kB]
Get:67 http://172.17.0.1/private buster-staging/main armhf libboost1.62-dev armhf 1.62.0+dfsg-4 [7009 kB]
Get:68 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62.0 armhf 1.62.0+dfsg-4 [232 kB]
Get:69 http://172.17.0.1/private buster-staging/main armhf libicu-dev armhf 57.1-6 [15.8 MB]
Get:70 http://172.17.0.1/private buster-staging/main armhf libboost-regex1.62-dev armhf 1.62.0+dfsg-4 [325 kB]
Get:71 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62.0 armhf 1.62.0+dfsg-4 [48.7 kB]
Get:72 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams1.62-dev armhf 1.62.0+dfsg-4 [57.7 kB]
Get:73 http://172.17.0.1/private buster-staging/main armhf libboost-iostreams-dev armhf 1.62.0.1+b6 [3694 B]
Get:74 http://172.17.0.1/private buster-staging/main armhf libbtf1 armhf 1:4.5.5-1 [19.0 kB]
Get:75 http://172.17.0.1/private buster-staging/main armhf libcamd2 armhf 1:4.5.5-1 [25.5 kB]
Get:76 http://172.17.0.1/private buster-staging/main armhf libccolamd2 armhf 1:4.5.5-1 [27.2 kB]
Get:77 http://172.17.0.1/private buster-staging/main armhf libcolamd2 armhf 1:4.5.5-1 [23.9 kB]
Get:78 http://172.17.0.1/private buster-staging/main armhf liblapack3 armhf 3.7.1-1 [1503 kB]
Get:79 http://172.17.0.1/private buster-staging/main armhf libmetis5 armhf 5.1.0.dfsg-5 [131 kB]
Get:80 http://172.17.0.1/private buster-staging/main armhf libcholmod3 armhf 1:4.5.5-1 [213 kB]
Get:81 http://172.17.0.1/private buster-staging/main armhf libnghttp2-14 armhf 1.24.0-1 [70.4 kB]
Get:82 http://172.17.0.1/private buster-staging/main armhf libpsl5 armhf 0.17.0-5 [42.0 kB]
Get:83 http://172.17.0.1/private buster-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-1 [54.2 kB]
Get:84 http://172.17.0.1/private buster-staging/main armhf libssh2-1 armhf 1.8.0-1 [126 kB]
Get:85 http://172.17.0.1/private buster-staging/main armhf libcurl3-gnutls armhf 7.52.1-5 [259 kB]
Get:86 http://172.17.0.1/private buster-staging/main armhf libcxsparse3 armhf 1:4.5.5-1 [47.2 kB]
Get:87 http://172.17.0.1/private buster-staging/main armhf libgsl2 armhf 2.3+dfsg-1 [722 kB]
Get:88 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.3+dfsg-1 [847 kB]
Get:89 http://172.17.0.1/private buster-staging/main armhf libhts2 armhf 1.4.1-5 [247 kB]
Get:90 http://172.17.0.1/private buster-staging/main armhf libhts-dev armhf 1.4.1-5 [338 kB]
Get:91 http://172.17.0.1/private buster-staging/main armhf libklu1 armhf 1:4.5.5-1 [47.4 kB]
Get:92 http://172.17.0.1/private buster-staging/main armhf liblapack-dev armhf 3.7.1-1 [1561 kB]
Get:93 http://172.17.0.1/private buster-staging/main armhf libldl2 armhf 1:4.5.5-1 [18.9 kB]
Get:94 http://172.17.0.1/private buster-staging/main armhf libumfpack5 armhf 1:4.5.5-1 [127 kB]
Get:95 http://172.17.0.1/private buster-staging/main armhf librbio2 armhf 1:4.5.5-1 [27.5 kB]
Get:96 http://172.17.0.1/private buster-staging/main armhf libspqr2 armhf 1:4.5.5-1 [62.7 kB]
Get:97 http://172.17.0.1/private buster-staging/main armhf libsuitesparse-dev armhf 1:4.5.5-1 [566 kB]
Get:98 http://172.17.0.1/private buster-staging/main armhf liblpsolve55-dev armhf 5.5.0.15-4 [350 kB]
Get:99 http://172.17.0.1/private buster-staging/main armhf libtinfo-dev armhf 6.0+20170715-2 [66.6 kB]
Get:100 http://172.17.0.1/private buster-staging/main armhf libncurses5-dev armhf 6.0+20170715-2 [246 kB]
Get:101 http://172.17.0.1/private buster-staging/main armhf libsqlite3-dev armhf 3.19.3-3 [622 kB]
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Setting up libtimedate-perl (2.3000-2) ...
Setting up libsigsegv2:armhf (2.11-1) ...
Setting up libldap-common (2.4.44+dfsg-8) ...
Setting up libbamtools2.4.0 (2.4.1+dfsg-1) ...
Setting up libblas-common (3.7.1-1) ...
Setting up libpsl5:armhf (0.17.0-5) ...
Setting up libgfortran3:armhf (6.4.0-1+rpi1) ...
Setting up groff-base (1.22.3-9) ...
Setting up libglib2.0-0:armhf (2.52.3-1) ...
No schema files found: doing nothing.
Setting up libsasl2-modules-db:armhf (2.1.27~101-g0780600+dfsg-3) ...
Setting up libgfortran-6-dev:armhf (6.4.0-1+rpi1) ...
Setting up libsasl2-2:armhf (2.1.27~101-g0780600+dfsg-3) ...
Setting up libtinfo-dev:armhf (6.0+20170715-2) ...
Setting up libsuitesparseconfig4:armhf (1:4.5.5-1) ...
Setting up gettext-base (0.19.8.1-2+b1) ...
Setting up libpipeline1:armhf (1.4.2-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-1) ...
Setting up libgsl2:armhf (2.3+dfsg-1) ...
Setting up m4 (1.4.18-1) ...
Setting up libicu57:armhf (57.1-6) ...
Setting up libbsd0:armhf (0.8.6-1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-3) ...
Setting up libmagic-mgc (1:5.30-1) ...
Setting up libmagic1:armhf (1:5.30-1) ...
Setting up libcroco3:armhf (0.6.12-1) ...
Setting up libboost-iostreams1.62.0:armhf (1.62.0+dfsg-4) ...
Setting up libncurses5-dev:armhf (6.0+20170715-2) ...
Setting up libssl1.0.2:armhf (1.0.2l-2) ...
Setting up libamd2:armhf (1:4.5.5-1) ...
Setting up ruby-did-you-mean (1.0.0-2) ...
Setting up libyaml-0-2:armhf (0.1.7-2) ...
Setting up libblas3 (3.7.1-1) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up libssh2-1:armhf (1.8.0-1) ...
Processing triggers for libc-bin (2.24-12) ...
Setting up autotools-dev (20161112.1) ...
Setting up libldap-2.4-2:armhf (2.4.44+dfsg-8) ...
Setting up libmetis5:armhf (5.1.0.dfsg-5) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libbam-dev (0.1.19-2) ...
Setting up libcolamd2:armhf (1:4.5.5-1) ...
Setting up rubygems-integration (1.11) ...
Setting up libccolamd2:armhf (1:4.5.5-1) ...
Setting up icu-devtools (57.1-6) ...
Setting up libkeyutils1:armhf (1.5.9-9) ...
Setting up bsdmainutils (9.0.12+nmu1) ...
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 (5.10.2-1) ...
Setting up autopoint (0.19.8.1-2) ...
Setting up ruby-power-assert (0.3.0-1) ...
Setting up zlib1g-dev:armhf (1:1.2.8.dfsg-5) ...
Setting up libfile-stripnondeterminism-perl (0.038-1) ...
Setting up libbtf1:armhf (1:4.5.5-1) ...
Setting up libldl2:armhf (1:4.5.5-1) ...
Setting up libcxsparse3:armhf (1:4.5.5-1) ...
Setting up gfortran-6 (6.4.0-1+rpi1) ...
Setting up gettext (0.19.8.1-2+b1) ...
Setting up libgsl-dev (2.3+dfsg-1) ...
Setting up liblapack3 (3.7.1-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up librbio2:armhf (1:4.5.5-1) ...
Setting up libboost-regex1.62.0:armhf (1.62.0+dfsg-4) ...
Setting up libcamd2:armhf (1:4.5.5-1) ...
Setting up libbamtools-dev (2.4.1+dfsg-1) ...
Setting up libklu1:armhf (1:4.5.5-1) ...
Setting up autoconf (2.69-10) ...
Setting up libicu-dev (57.1-6) ...
Setting up file (1:5.30-1) ...
Setting up libkrb5support0:armhf (1.15.1-2) ...
Setting up libcholmod3:armhf (1:4.5.5-1) ...
Setting up intltool-debian (0.35.0+20060710.4) ...
Setting up automake (1:1.15.1-2) ...
update-alternatives: using /usr/bin/automake-1.15 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.7.6.1-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libspqr2:armhf (1:4.5.5-1) ...
Setting up libtool (2.4.6-2) ...
Setting up gfortran (4:6.3.0-4d1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libk5crypto3:armhf (1.15.1-2) ...
Setting up po-debconf (1.0.20) ...
Setting up libblas-dev (3.7.1-1) ...
update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode
Setting up libboost-regex1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up libboost-iostreams1.62-dev:armhf (1.62.0+dfsg-4) ...
Setting up libumfpack5:armhf (1:4.5.5-1) ...
Setting up libboost-iostreams-dev:armhf (1.62.0.1+b6) ...
Setting up libkrb5-3:armhf (1.15.1-2) ...
Setting up liblapack-dev (3.7.1-1) ...
update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode
Setting up libgssapi-krb5-2:armhf (1.15.1-2) ...
Setting up libsuitesparse-dev:armhf (1:4.5.5-1) ...
Setting up libcurl3-gnutls:armhf (7.52.1-5) ...
Setting up liblpsolve55-dev (5.5.0.15-4) ...
Setting up libhts2:armhf (1.4.1-5) ...
Setting up libhts-dev:armhf (1.4.1-5) ...
Setting up dh-autoreconf (14) ...
Setting up rake (12.0.0-1) ...
Setting up ruby2.3 (2.3.3-1) ...
Setting up dh-strip-nondeterminism (0.038-1) ...
Setting up ruby (1:2.3.3) ...
Setting up debhelper (10.6.4) ...
Setting up ruby-test-unit (3.2.5-1) ...
Setting up asciidoctor (1.5.5-1) ...
Setting up libruby2.3:armhf (2.3.3-1) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.24-12) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.28-6 dpkg-dev_1.18.24 g++-6_6.4.0-1+rpi1 gcc-6_6.4.0-1+rpi1 libc6-dev_2.24-12 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch
Package versions: adduser_3.115 apt_1.5~beta1+b3 asciidoctor_1.5.5-1 autoconf_2.69-10 automake_1:1.15.1-2 autopoint_0.19.8.1-2 autotools-dev_20161112.1 base-files_10+rpi1 base-passwd_3.5.43 bash_4.4-5 binutils_2.28-6 bsdmainutils_9.0.12+nmu1 bsdutils_1:2.29.2-2+rpi1 build-essential_12.3 bzip2_1.0.6-8.1 ca-certificates_20161130+nmu1 coreutils_8.26-3 cpio_2.11+dfsg-6 cpp_4:6.3.0-4d1 cpp-6_6.4.0-1+rpi1 dash_0.5.8-2.5 debconf_1.5.63 debhelper_10.6.4 debianutils_4.8.1.1 dh-autoreconf_14 dh-strip-nondeterminism_0.038-1 diffutils_1:3.5-3 dmsetup_2:1.02.137-2 dpkg_1.18.24 dpkg-dev_1.18.24 e2fslibs_1.43.4-2 e2fsprogs_1.43.4-2 fakeroot_1.21-3.1 file_1:5.30-1 findutils_4.6.0+git+20170606-3 g++_4:6.3.0-4d1 g++-6_6.4.0-1+rpi1 gcc_4:6.3.0-4d1 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_4.9.3-14 gcc-5-base_5.4.1-4 gcc-6_6.4.0-1+rpi1 gcc-6-base_6.4.0-1+rpi1 gcc-7-base_7.1.0-9+rpi1 gettext_0.19.8.1-2+b1 gettext-base_0.19.8.1-2+b1 gfortran_4:6.3.0-4d1 gfortran-6_6.4.0-1+rpi1 gnupg_2.1.18-8 gnupg-agent_2.1.18-8 gpgv_2.1.18-8 grep_3.1-2 groff-base_1.22.3-9 gzip_1.6-5 hostname_3.18 icu-devtools_57.1-6 init-system-helpers_1.48 initramfs-tools_0.130 initramfs-tools-core_0.130 intltool-debian_0.35.0+20060710.4 klibc-utils_2.0.4-9+rpi1 kmod_24-1 libacl1_2.2.52-3 libamd2_1:4.5.5-1 libapparmor1_2.11.0-6 libapt-pkg5.0_1.5~beta1+b3 libarchive-zip-perl_1.59-1 libasan3_6.4.0-1+rpi1 libassuan0_2.4.3-2 libatomic1_7.1.0-9+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.7.7-1 libaudit1_1:2.7.7-1 libbam-dev_0.1.19-2 libbamtools-dev_2.4.1+dfsg-1 libbamtools2.4.0_2.4.1+dfsg-1 libblas-common_3.7.1-1 libblas-dev_3.7.1-1 libblas3_3.7.1-1 libblkid1_2.29.2-2+rpi1 libboost-iostreams-dev_1.62.0.1+b6 libboost-iostreams1.62-dev_1.62.0+dfsg-4 libboost-iostreams1.62.0_1.62.0+dfsg-4 libboost-regex1.62-dev_1.62.0+dfsg-4 libboost-regex1.62.0_1.62.0+dfsg-4 libboost1.62-dev_1.62.0+dfsg-4 libbsd0_0.8.6-1 libbtf1_1:4.5.5-1 libbz2-1.0_1.0.6-8.1 libc-bin_2.24-12 libc-dev-bin_2.24-12 libc6_2.24-12 libc6-dev_2.24-12 libcamd2_1:4.5.5-1 libcap-ng0_0.7.7-3 libcap2_1:2.25-1 libcc1-0_7.1.0-9+rpi1 libccolamd2_1:4.5.5-1 libcholmod3_1:4.5.5-1 libcolamd2_1:4.5.5-1 libcomerr2_1.43.4-2 libcroco3_0.6.12-1 libcryptsetup4_2:1.7.3-4 libcurl3-gnutls_7.52.1-5 libcxsparse3_1:4.5.5-1 libdb5.3_5.3.28-12 libdbus-1-3_1.10.20-1 libdebconfclient0_0.229 libdevmapper1.02.1_2:1.02.137-2 libdpkg-perl_1.18.24 libdrm2_2.4.81-2+rpi1 libfakeroot_1.21-3.1 libfdisk1_2.29.2-2+rpi1 libffi6_3.2.1-6 libfile-stripnondeterminism-perl_0.038-1 libgcc-6-dev_6.4.0-1+rpi1 libgcc1_1:7.1.0-9+rpi1 libgcrypt20_1.7.8-2 libgdbm3_1.8.3-14 libgfortran-6-dev_6.4.0-1+rpi1 libgfortran3_6.4.0-1+rpi1 libglib2.0-0_2.52.3-1 libgmp10_2:6.1.2+dfsg-1 libgnutls30_3.5.14-2 libgomp1_7.1.0-9+rpi1 libgpg-error0_1.27-3 libgsl-dev_2.3+dfsg-1 libgsl2_2.3+dfsg-1 libgssapi-krb5-2_1.15.1-2 libhogweed4_3.3-1 libhts-dev_1.4.1-5 libhts2_1.4.1-5 libicu-dev_57.1-6 libicu57_57.1-6 libidn11_1.33-1 libidn2-0_2.0.2-1 libip4tc0_1.6.1-2 libisl15_0.18-1 libk5crypto3_1.15.1-2 libkeyutils1_1.5.9-9 libklibc_2.0.4-9+rpi1 libklu1_1:4.5.5-1 libkmod2_24-1 libkrb5-3_1.15.1-2 libkrb5support0_1.15.1-2 libksba8_1.3.5-2 liblapack-dev_3.7.1-1 liblapack3_3.7.1-1 libldap-2.4-2_2.4.44+dfsg-8 libldap-common_2.4.44+dfsg-8 libldl2_1:4.5.5-1 liblpsolve55-dev_5.5.0.15-4 liblz4-1_0.0~r131-2 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.30-1 libmagic1_1:5.30-1 libmetis5_5.1.0.dfsg-5 libmount1_2.29.2-2+rpi1 libmpc3_1.0.3-1 libmpfr4_3.1.5-1 libncurses5_6.0+20170715-2 libncurses5-dev_6.0+20170715-2 libncursesw5_6.0+20170715-2 libnettle6_3.3-1 libnghttp2-14_1.24.0-1 libnih-dbus1_1.0.3-8 libnih1_1.0.3-8 libnpth0_1.5-2 libp11-kit0_0.23.7-3 libpam-modules_1.1.8-3.6 libpam-modules-bin_1.1.8-3.6 libpam-runtime_1.1.8-3.6 libpam0g_1.1.8-3.6 libpcre3_2:8.39-3 libperl5.24_5.24.1-7 libperl5.26_5.26.0-4 libpipeline1_1.4.2-1 libplymouth4_0.9.2-4 libpng16-16_1.6.30-2 libprocps6_2:3.3.12-3 libpsl5_0.17.0-5 librbio2_1:4.5.5-1 libreadline5_5.2+dfsg-3 libreadline7_7.0-3 librtmp1_2.4+20151223.gitfa8646d.1-1 libruby2.3_2.3.3-1 libsasl2-2_2.1.27~101-g0780600+dfsg-3 libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3 libseccomp2_2.3.1-2.1 libselinux1_2.6-3 libsemanage-common_2.6-2 libsemanage1_2.6-2 libsepol1_2.6-2 libsigsegv2_2.11-1 libsmartcols1_2.29.2-2+rpi1 libspqr2_1:4.5.5-1 libsqlite3-0_3.19.3-3 libsqlite3-dev_3.19.3-3 libss2_1.43.4-2 libssh2-1_1.8.0-1 libssl1.0.2_1.0.2l-2 libssl1.1_1.1.0f-3 libstdc++-6-dev_6.4.0-1+rpi1 libstdc++6_7.1.0-9+rpi1 libsuitesparse-dev_1:4.5.5-1 libsuitesparseconfig4_1:4.5.5-1 libsystemd0_233-10 libtasn1-6_4.12-2 libtimedate-perl_2.3000-2 libtinfo-dev_6.0+20170715-2 libtinfo5_6.0+20170715-2 libtool_2.4.6-2 libubsan0_7.1.0-9+rpi1 libudev1_233-10 libumfpack5_1:4.5.5-1 libunistring2_0.9.7-2 libustr-1.0-1_1.0.4-6 libuuid1_2.29.2-2+rpi1 libxml2_2.9.4+dfsg1-3 libyaml-0-2_0.1.7-2 linux-base_4.5 linux-libc-dev_3.18.5-1~exp1+rpi19+stretch login_1:4.4-4.1 lsb-base_9.20161125+rpi1 m4_1.4.18-1 make_4.1-9.1 makedev_2.3.1-93 man-db_2.7.6.1-2 mawk_1.3.3-17 mount_2.29.2-2+rpi1 mountall_2.54 multiarch-support_2.24-12 ncurses-base_6.0+20170715-2 ncurses-bin_6.0+20170715-2 openssl_1.1.0f-3 passwd_1:4.4-4.1 patch_2.7.5-1 perl_5.26.0-4 perl-base_5.26.0-4 perl-modules-5.24_5.24.1-7 perl-modules-5.26_5.26.0-4 pinentry-curses_1.0.0-2 plymouth_0.9.2-4 po-debconf_1.0.20 procps_2:3.3.12-3 rake_12.0.0-1 raspbian-archive-keyring_20120528.2 readline-common_7.0-3 ruby_1:2.3.3 ruby-did-you-mean_1.0.0-2 ruby-minitest_5.10.2-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_0.3.0-1 ruby-test-unit_3.2.5-1 ruby2.3_2.3.3-1 rubygems-integration_1.11 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.4-1 sensible-utils_0.0.9+nmu1 systemd_233-10 sysvinit-utils_2.88dsf-59.9 tar_1.29b-2 tzdata_2017b-2 udev_233-10 util-linux_2.29.2-2+rpi1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.8.dfsg-5 zlib1g-dev_1:1.2.8.dfsg-5
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sun Dec 11 11:08:13 2016 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./augustus_3.2.3+dfsg-1.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.2.3+dfsg
dpkg-source: info: unpacking augustus_3.2.3+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.2.3+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 disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 3.2.3+dfsg-1+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-c0958a79-3130-4666-bc28-9ed28cf5528c
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.2.3+dfsg-1+b2
dpkg-buildpackage: info: source distribution buster-staging
dpkg-source --before-build augustus-3.2.3+dfsg
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --parallel
dh_testdir
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping/src clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/joingenes'
rm -rf *o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/joingenes'
rm -rf bin
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
dh_autoreconf_clean
dh_clean
debian/rules build-arch
dh build-arch --parallel
dh_testdir -a -O--parallel
dh_update_autotools_config -a -O--parallel
dh_autoreconf -a -O--parallel
dh_auto_configure -a -O--parallel
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
mkdir -p bin
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/bam2hints'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c bam2hints.cc -o bam2hints.o -I/usr/include/bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz
cp bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/homGeneMapping/src'
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -Wl,-z,relro -Wl,-z,now -o gene.o gene.cc -I../include
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -Wl,-z,relro -Wl,-z,now -o genome.o genome.cc -I../include
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o homGeneMapping main.cc gene.o genome.o -I../include
cp homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/checkTargetSortedness
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/checkTargetSortedness'
gcc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c checkTargetSortedness.c -o checkTargetSortedness.o -I/usr/include/samtools -I.
gcc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now checkTargetSortedness.o -o checkTargetSortedness -lbam -lcurses -lm -lz -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/joingenes'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_transcript.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_ios.cpp
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.o jg_transcript.o jg_ios.o -o joingenes -Wl,-z,relro -Wl,-z,now
cp joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/joingenes'
dh_auto_build
make -j4
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
mkdir -p bin
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o genbank.o genbank.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o properties.o properties.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_profile.o pp_profile.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include
pp_profile.cc:91:10: warning: 'std::ostream& PP::operator<<(std::ostream&, const PP::Column&)' has not been declared within PP
ostream& PP::operator<<(ostream& strm, const Column& c) {
^~
In file included from pp_profile.cc:14:0:
../include/pp_profile.hh:274:18: note: only here as a friend
friend ostream& operator<<(ostream&, const Column&);
^~~~~~~~
pp_profile.cc:97:10: warning: 'std::istream& PP::operator>>(std::istream&, PP::Column&)' has not been declared within PP
istream& PP::operator>>(istream& strm, Column& c) {
^~
In file included from pp_profile.cc:14:0:
../include/pp_profile.hh:275:18: note: only here as a friend
friend istream& operator>>(istream&, Column& c);
^~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include
In file included from /usr/include/c++/6/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++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PP::Column; _Alloc = std::allocator<PP::Column>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<PP::Column>::iterator {aka __gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/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++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_vector.h: In member function 'bool PP::Block::initThresholds()':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'void PP::Profile::calcGlobalThresh(const std::vector<std::vector<Dist> >&)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PP::BonusProbEntry; _Alloc = std::allocator<PP::BonusProbEntry>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<PP::BonusProbEntry>::iterator {aka __gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_vector.h: In member function 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/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++/6/bits/stl_tree.h:2282:5: 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> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:2282:5: 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> >}' will change in GCC 7.1
/usr/include/c++/6/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++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
{ _M_erase_aux(__first, __last); }
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = PP::Block; _Alloc = std::allocator<PP::Block>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<PP::Block>::iterator {aka __gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::_Alloc_node; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/6/bits/stl_tree.h:1989:7: 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> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h: In member function 'void ViterbiSubmapType::eraseAndDecCounts(ViterbiSubmapType::iterator) const':
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h: In member function 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)':
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include
/usr/include/c++/6/bits/stl_tree.h: In member function 'bool ViterbiSubmapType::setMax(SubstateId, Double, ViterbiSubmapType*) const':
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h: In member function 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)':
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
{ _M_erase_aux(__first, __last); }
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
In file included from /usr/include/c++/6/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++/6/bits/stl_vector.h: In member function 'void PP::Profile::parse_stream(std::istream&)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h: In member function 'void PP::BonusProbType::mergeIntoSubmap(int, ViterbiSubmapType&, SubstateIdMap*)':
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)':
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
{ _M_erase_aux(__first, __last); }
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)':
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
{ _M_erase_aux(__first, __last); }
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include
In file included from /usr/include/c++/6/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++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::_Alloc_node; _Key = int; _Val = std::pair<const int, LLDouble>; _KeyOfValue = std::_Select1st<std::pair<const int, LLDouble> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/6/bits/stl_tree.h:1989:7: 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> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_vector.h: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, LLDouble>, std::_Select1st<std::pair<const int, LLDouble> >, std::less<int>, std::allocator<std::pair<const int, LLDouble> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const int, LLDouble> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include
In file included from /usr/include/c++/6/vector:69:0,
from ../include/types.hh:35,
from types.cc:18:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from types.cc:18:
/usr/include/c++/6/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++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from statemodel.cc:16:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator {aka __gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator {aka __gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from statemodel.cc:16:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void StateModel::initPredecessors(Matrix<LLDouble>&, int)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void Constant::init()':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/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++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/6/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++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from ../include/types.hh:37,
from types.cc:18:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In function 'Double quantile(const std::vector<LLDouble>&, float)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o evaluation.o evaluation.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include
In file included from /usr/include/c++/6/vector:69:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from motif.cc:14:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from motif.cc:14:
/usr/include/c++/6/bits/stl_vector.h: In member function 'Double Motif::getProbThreshold(double, int)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o hints.o hints.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o extrinsicinfo.o extrinsicinfo.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include
In file included from /usr/include/c++/6/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++/6/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++/6/bits/list.tcc:307:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' will change in GCC 7.1
list<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:307:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc: In static member function 'static StatePath* StatePath::condenseStatePath(StatePath*)':
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' will change in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o intronmodel.o intronmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include
/usr/include/c++/6/bits/list.tcc: In copy constructor 'Gene::Gene(const Gene&)':
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/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++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/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++/6/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++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/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++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from gene.cc:21:
/usr/include/c++/6/bits/stl_vector.h: In function 'void examineBaseCountOfGeneSeq(AnnoSequence*)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include
In file included from /usr/include/c++/6/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/intronmodel.hh:17,
from intronmodel.cc:26:
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void IntronModel::readProbabilities(int)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void IntronModel::readAllParameters()':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/igenicmodel.hh:20,
from igenicmodel.cc:14:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/igenicmodel.hh:20,
from igenicmodel.cc:14:
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void IGenicModel::readProbabilities(int)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/exonmodel.hh:22,
from exonmodel.cc:25:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/exonmodel.hh:22,
from exonmodel.cc:25:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, std::vector<_Tp, _Alloc>::value_type) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void ExonModel::readAllParameters()':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/list:64:0,
from ../include/hints.hh:22,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/6/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<Feature>; _Tp = Feature; _Alloc = std::allocator<Feature>]':
/usr/include/c++/6/bits/list.tcc:307:7: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
list<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:307:7: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc: In member function 'void SequenceFeatureCollection::warnInconsistentHints(AnnoSequence*)':
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void IGenicModel::readAllParameters()':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc: In member function 'void SequenceFeatureCollection::cleanRedundantFeatures()':
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrmodel.o utrmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include
In file included from /usr/include/c++/6/vector:69:0,
from ../include/types.hh:35,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include
In file included from /usr/include/c++/6/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++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::_Alloc_node; _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity<Feature>; _Compare = std::less<Feature>; _Alloc = std::allocator<Feature>]':
/usr/include/c++/6/bits/stl_tree.h:1989:7: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/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++/6/bits/stl_algo.h:5201:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__set_difference(_InputIterator1 __first1, _InputIterator1 __last1,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:5201:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5201:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5201:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator {aka std::_Rb_tree_const_iterator<Feature>}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
In file included from /usr/include/c++/6/list:64:0,
from ../include/hints.hh:22,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/6/bits/list.tcc: In member function 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)':
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/bits/stl_tree.h:2250:4: 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>}' will change in GCC 7.1
_M_insert_unique_(end(), *__first, __an);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/list:64:0,
from ../include/hints.hh:22,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/bits/stl_tree.h:2250:4: 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>}' will change in GCC 7.1
_M_insert_unique_(end(), *__first, __an);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/list:64:0,
from ../include/hints.hh:22,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/bits/stl_tree.h:2250:4: 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>}' will change in GCC 7.1
_M_insert_unique_(end(), *__first, __an);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/list:64:0,
from ../include/hints.hh:22,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/bits/stl_tree.h:2250:4: 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>}' will change in GCC 7.1
_M_insert_unique_(end(), *__first, __an);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
__gnu_cxx::__ops::__iter_less_iter());
^
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:5266:44: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/list:64:0,
from ../include/hints.hh:22,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
_M_assign_dispatch(__x.begin(), __x.end(), __false_type());
^~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
/usr/include/c++/6/bits/list.tcc:285:4: note: parameter passing for argument of type 'std::_List_const_iterator<Feature>' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:69:0,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = ViterbiSubmapType; _Alloc = std::allocator<ViterbiSubmapType>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<ViterbiSubmapType>::iterator {aka __gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = ViterbiEntryType; _Alloc = std::allocator<ViterbiEntryType>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<ViterbiEntryType>::iterator {aka __gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void ViterbiColumnType::addState(int, signed char)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/map:60:0,
from ../include/types.hh:38,
from ../include/vitmatrix.hh:14,
from vitmatrix.cc:10:
/usr/include/c++/6/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++/6/bits/stl_tree.h:2282:5: 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> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:2282:5: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h: In member function 'void ViterbiSubmapType::useMaximum(Double&)':
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
{ _M_erase_aux(__first, __last); }
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
{ _M_erase_aux(__first, __last); }
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h: In member function 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)':
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
{ _M_erase_aux(__first, __last); }
^~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h:1075:9: 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> >}' will change in GCC 7.1
/usr/include/c++/6/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique_(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const _Val&, _NodeGen&) [with _NodeGen = std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::_Alloc_node; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/6/bits/stl_tree.h:1989:7: 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> >}' will change in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_tree.h: In member function 'void ViterbiSubmapType::merge(ViterbiSubmapType&, Double)':
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h: In member function 'void ViterbiSubmapType::registerPredecessors()':
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
/usr/include/c++/6/bits/stl_tree.h:996:43: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator {aka std::_Rb_tree_const_iterator<std::pair<const SubstateId, ViterbiSubmapEntry> >}' will change in GCC 7.1
return _M_insert_unique_(__pos, __x, __an);
^
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from ../include/hints.hh:18,
from ../include/extrinsicinfo.hh:23,
from extrinsicinfo.cc:31:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void FeatureCollection::readTypeInfo(std::istream&)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include
In file included from /usr/include/c++/6/vector:69:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void Parameters::addMerkmal(Double*, double)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:69:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void BinnedMMGroup::read(std::ifstream&)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/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++/6/bits/stl_algo.h:1818:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/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++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1837:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrmodel.cc:23:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, std::vector<_Tp, _Alloc>::value_type) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/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++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In member function 'void BinnedMMGroup::trainBins(int)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/bits/stl_algo.h:61:0,
from /usr/include/c++/6/algorithm:62,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/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++/6/bits/stl_heap.h:209:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/6/algorithm:62:0,
from ../include/types.hh:37,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/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++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_algo.h:1937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
/usr/include/c++/6/bits/stl_algo.h:1951:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h: In static member function 'static std::vector<double> CRF::capOutliers(std::vector<double>)':
/usr/include/c++/6/bits/stl_algo.h:1965:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__introsort_loop(__first, __last,
^~~
/usr/include/c++/6/bits/stl_algo.h:1882:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
^~~
/usr/include/c++/6/bits/stl_algo.h:1887:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
^~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from ../include/merkmal.hh:16,
from merkmal.cc:13:
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/motif.hh:20,
from ../include/gene.hh:14,
from ../include/mea.hh:4,
from mea.cc:1:
/usr/include/c++/6/bits/stl_vector.h: In constructor 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = int; V = double]':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void CRF::improvedIterativeScaling(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o randseqaccess.o randseqaccess.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o fasta.o fasta.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o ncmodel.o ncmodel.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o commontrain.o commontrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include
In file included from /usr/include/c++/6/vector:69:0,
from ../include/types.hh:35,
from ../include/commontrain.hh:14,
from commontrain.cc:10:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from ../include/commontrain.hh:14,
from commontrain.cc:10:
/usr/include/c++/6/bits/stl_vector.h: In member function 'int Smooth::geoCutOff(const std::vector<long int>&, std::vector<LLDouble>&)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include
In file included from /usr/include/c++/6/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/igenicmodel.hh:20,
from igenictrain.cc:13:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_vector.h: In member function 'void NcModel::computeLengthDistributions()':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/igenicmodel.hh:20,
from igenictrain.cc:13:
/usr/include/c++/6/bits/stl_vector.h: In member function 'virtual void IGenicModel::buildModel(const AnnoSequence*, int)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exontrain.o exontrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include
In file included from /usr/include/c++/6/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++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_vector.h: In member function 'void IntronModel::makeDSSProbs()':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include
In file included from /usr/include/c++/6/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++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/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++/6/bits/stl_vector.h: In member function 'void IntronModel::buildProbabilities(const AnnoSequence*)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o prepareAlign pp_prepare_align.cc
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include
In file included from /usr/include/c++/6/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++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/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++/6/bits/stl_vector.h: In member function 'void ExonModel::computeLowerOrderPats()':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'void ExonModel::buildProbabilities()':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
echo "-Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security " > cxxflags
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+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
cp prepareAlign ../bin/
In file included from /usr/include/c++/6/vector:69:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrtrain.cc:15:
/usr/include/c++/6/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++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/6/bits/vector.tcc:449:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
In file included from /usr/include/c++/6/vector:64:0,
from ../include/matrix.hh:26,
from ../include/statemodel.hh:15,
from ../include/utrmodel.hh:17,
from utrtrain.cc:15:
/usr/include/c++/6/bits/stl_vector.h: In member function 'void UtrModel::buildTSSModel(const AnnoSequence*)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In member function 'void UtrModel::buildProbabilities(const AnnoSequence*)':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void UtrModel::computeLengthDistributions()':
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
/usr/include/c++/6/bits/stl_vector.h:1074:9: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator {aka __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >}' will change in GCC 7.1
{ _M_fill_insert(__position, __n, __x); }
^~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -Wno-strict-overflow -ansi -pedantic -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+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
cp augustus ../bin/
In file included from /usr/include/c++/6/vector:69:0,
from ../include/types.hh:35,
from etraining.cc:12:
/usr/include/c++/6/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, const _Tp&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/6/bits/vector.tcc:326:5: note: parameter passing for argument of type 'std::vector<double>::iterator {aka __gnu_cxx::__normal_iterator<double*, std::vector<double> >}' will change in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/6/vector:64:0,
from ../include/types.hh:35,
from etraining.cc:12:
/usr/include/c++/6/bits/stl_vector.h: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]':
/usr/include/c++/6/bits/stl_vector.h:926:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' will change in GCC 7.1
_M_insert_aux(end(), __x);
^~~~~~~~~~~~~
cp fastBlockSearch ../bin/
cp etraining ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/bam2hints'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'bam2hints' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/compileSpliceCands'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
gcc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90
s = malloc(3500000000);
^
compileSpliceCands.c: 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-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
gcc -o compileSpliceCands compileSpliceCands.o list.o -Wl,-z,relro -Wl,-z,now;
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/compileSpliceCands'
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/filterBam/src'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.2.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
cp filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/joingenes'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs/joingenes'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg/auxprogs'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
dh_auto_test -a -O--parallel
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --parallel
dh_testroot -a -O--parallel
dh_prep -a -O--parallel
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
mkdir -p debian/augustus/usr/bin
install bin/* debian/augustus/usr/bin
install auxprogs/checkTargetSortedness/checkTargetSortedness \
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/*
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-3.2.3+dfsg'
dh_installdocs -a -O--parallel
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
dh_installchangelogs -k HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
dh_installman -a -O--parallel
dh_perl -a -O--parallel
dh_link -a -O--parallel
dh_strip_nondeterminism -a -O--parallel
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.2.3+dfsg'
dh_fixperms -a -O--parallel
dh_missing -a -O--parallel
dh_strip -a -O--parallel
dh_makeshlibs -a -O--parallel
dh_shlibdeps -a -O--parallel
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/fastBlockSearch contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/augustus contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/bam2hints contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: 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/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/augustus/usr/bin/checkTargetSortedness was not linked against libtinfo.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 was not linked against libncurses.so.5 (it uses none of the library's symbols)
dh_installdeb -a -O--parallel
dh_gencontrol -a -O--parallel
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dpkg-gencontrol: warning: package augustus: unused substitution variable ${perl:Depends}
dh_md5sums -a -O--parallel
dh_builddeb -a -O--parallel
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.2.3+dfsg-1+b2_armhf.deb'.
dpkg-deb: building package 'augustus' in '../augustus_3.2.3+dfsg-1+b2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../augustus_3.2.3+dfsg-1+b2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build augustus-3.2.3+dfsg
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2017-07-29T12:07:28Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.2.3+dfsg-1+b2_armhf.changes:
---------------------------------------
Format: 1.8
Date: Sun, 11 Dec 2016 10:25:18 +0000
Source: augustus (3.2.3+dfsg-1)
Binary: augustus augustus-data augustus-doc
Binary-Only: yes
Architecture: armhf
Version: 3.2.3+dfsg-1+b2
Distribution: buster-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
augustus - gene prediction in eukaryotic genomes
augustus-data - data files for AUGUSTUS
augustus-doc - documentation files for AUGUSTUS
Changes:
augustus (3.2.3+dfsg-1+b2) buster-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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6f8a436d0df3db8650c85ab014649d2d2e93b936 884540 augustus_3.2.3+dfsg-1+b2_armhf.deb
0f97f979803944105e2d1c7ac2c84e5a1982ffce 7235 augustus_3.2.3+dfsg-1_armhf.buildinfo
Checksums-Sha256:
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858035e0ac47198a671cf7ff066d77dc95fb740de6882742ffac47936396b601 884540 augustus_3.2.3+dfsg-1+b2_armhf.deb
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Files:
ecd2483776d63e2f6c82f39506e1da19 14642594 debug extra augustus-dbgsym_3.2.3+dfsg-1+b2_armhf.deb
6d32a4d69909e878c55cbf96a147c48a 884540 science optional augustus_3.2.3+dfsg-1+b2_armhf.deb
ec48a24f227e4b8df837d9a5480aed6d 7235 science optional augustus_3.2.3+dfsg-1_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.2.3+dfsg-1+b2_armhf.deb
-----------------------------------------
new debian package, version 2.0.
size 14642594 bytes: control archive=913 bytes.
732 bytes, 12 lines control
954 bytes, 9 lines md5sums
Package: augustus-dbgsym
Source: augustus (3.2.3+dfsg-1)
Version: 3.2.3+dfsg-1+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 14829
Depends: augustus (= 3.2.3+dfsg-1+b2)
Section: debug
Priority: extra
Description: Debug symbols for augustus
Build-Ids: 09294545dda45f75c49619dd9d5fc21fc87bd3c0 576291a121d2778af65af489093fbff8f4350af7 5a2fb858ec07ad3fe1907fde3b8b3cca1b0d5f6f 6c8699f9353d448d7716a3576fd596fa6f6837df 716c77e2c4edfaa1641b6d967dbda25ed8ad01c9 7ec437db979e87e592d883c891f13fcace92ad1d b1539f36a6d25da60e89e61df5eeaa84590c9fbe b59fae5cceb143b4c732685ee9d91a1878c42230 f4eda2fd872f91f82d0a43837bdafd2701dba292
drwxr-xr-x root/root 0 2016-12-11 10:25 ./
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/lib/
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/lib/debug/
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/lib/debug/.build-id/09/
-rw-r--r-- root/root 5674052 2016-12-11 10:25 ./usr/lib/debug/.build-id/09/294545dda45f75c49619dd9d5fc21fc87bd3c0.debug
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/lib/debug/.build-id/57/
-rw-r--r-- root/root 108956 2016-12-11 10:25 ./usr/lib/debug/.build-id/57/6291a121d2778af65af489093fbff8f4350af7.debug
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/lib/debug/.build-id/5a/
-rw-r--r-- root/root 948692 2016-12-11 10:25 ./usr/lib/debug/.build-id/5a/2fb858ec07ad3fe1907fde3b8b3cca1b0d5f6f.debug
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/lib/debug/.build-id/6c/
-rw-r--r-- root/root 18708 2016-12-11 10:25 ./usr/lib/debug/.build-id/6c/8699f9353d448d7716a3576fd596fa6f6837df.debug
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/lib/debug/.build-id/71/
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augustus_3.2.3+dfsg-1+b2_armhf.deb
----------------------------------
new debian package, version 2.0.
size 884540 bytes: control archive=4412 bytes.
1280 bytes, 22 lines control
8605 bytes, 114 lines md5sums
Package: augustus
Source: augustus (3.2.3+dfsg-1)
Version: 3.2.3+dfsg-1+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3723
Depends: libbamtools2.4.0, libc6 (>= 2.15), libgcc1 (>= 1:4.0), libncurses5 (>= 6), libstdc++6 (>= 6), libtinfo5 (>= 6), zlib1g (>= 1:1.2.3.3), libgsl2, augustus-data, libhts1
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 2016-12-11 10:25 ./
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drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/bin/
-rwxr-xr-x root/root 1085680 2016-12-11 10:25 ./usr/bin/augustus
-rwxr-xr-x root/root 26584 2016-12-11 10:25 ./usr/bin/bam2hints
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-rwxr-xr-x root/root 120372 2016-12-11 10:25 ./usr/bin/joingenes
-rwxr-xr-x root/root 26184 2016-12-11 10:25 ./usr/bin/prepareAlign
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/share/
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/share/augustus/
drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/share/augustus/scripts/
-rw-r--r-- root/root 12539 2016-12-11 10:25 ./usr/share/augustus/scripts/README.autoAug
-rw-r--r-- root/root 12247 2016-12-11 10:25 ./usr/share/augustus/scripts/SplicedAlignment.pm
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-rw-r--r-- root/root 195 2016-12-11 10:25 ./usr/share/augustus/scripts/autoRun.pathInfo
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drwxr-xr-x root/root 0 2016-12-11 10:25 ./usr/share/doc/
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-rw-r--r-- root/root 3128 2016-12-11 10:00 ./usr/share/doc/augustus/copyright
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 685856
Build-Time: 797
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 606
Job: augustus_3.2.3+dfsg-1
Machine Architecture: armhf
Package: augustus
Package-Time: 1468
Source-Version: 3.2.3+dfsg-1
Space: 685856
Status: successful
Version: 3.2.3+dfsg-1+b2
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Finished at 2017-07-29T12:07:28Z
Build needed 00:24:28, 685856k disc space