augustus →
3.3.3+dfsg-4 →
armhf → 2020-10-09 05:35:29
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| augustus 3.3.3+dfsg-4 (armhf) Fri, 09 Oct 2020 04:55:16 +0000 |
+==============================================================================+
Package: augustus
Version: 3.3.3+dfsg-4
Source Version: 3.3.3+dfsg-4
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-06871c0d-0a82-4200-8c51-97de124468aa' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.4 MB in 25s (962 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'augustus' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/augustus.git
Please use:
git clone https://salsa.debian.org/med-team/augustus.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 66.2 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main augustus 3.3.3+dfsg-4 (dsc) [2293 B]
Get:2 http://172.17.0.1/private bullseye-staging/main augustus 3.3.3+dfsg-4 (tar) [66.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main augustus 3.3.3+dfsg-4 (diff) [19.3 kB]
Fetched 66.2 MB in 6s (11.9 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/augustus-LhdDhW/augustus-3.3.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/augustus-LhdDhW' 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-UdlUwo/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-UdlUwo/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-UdlUwo/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-UdlUwo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ Packages [433 B]
Fetched 2109 B in 1s (2639 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils libpam-cap netbase sensible-utils
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 37 not upgraded.
Need to get 856 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 856 B in 0s (19.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12554 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libssl-dev, asciidoctor
Filtered Build-Depends: debhelper-compat (= 13), libsqlite3-dev, libboost-iostreams-dev, zlib1g-dev, libgsl-dev, liblpsolve55-dev, libbamtools-dev, libbam-dev, libbz2-dev, lzma-dev, libhts-dev, libncurses5-dev, libssl-dev, asciidoctor
dpkg-deb: building package 'sbuild-build-depends-augustus-dummy' in '/<<BUILDDIR>>/resolver-UdlUwo/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-UdlUwo/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ Sources [571 B]
Get:5 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ Packages [652 B]
Fetched 2556 B in 1s (3410 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install augustus build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev binutils
binutils-arm-linux-gnueabihf binutils-common ca-certificates cpp-10
debhelper dh-autoreconf dh-strip-nondeterminism dwz file g++-10 gcc-10
gcc-10-base gettext gettext-base groff-base icu-devtools intltool-debian
libamd2 libarchive-zip-perl libasan6 libatomic1 libbam-dev libbamtools-dev
libbamtools2.5.1 libbinutils libblas-dev libblas3 libboost-iostreams-dev
libboost-iostreams1.71-dev libboost-regex1.71-dev libboost-regex1.71.0
libboost1.71-dev libbrotli1 libbtf1 libbz2-dev libcamd2 libcc1-0 libccolamd2
libcholmod3 libcolamd2 libcroco3 libctf0 libcurl3-gnutls libcurl4-gnutls-dev
libcxsparse3 libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libgcc-10-dev libgcc-s1 libgfortran5
libglib2.0-0 libgomp1 libgraphblas3 libgsl-dev libgsl25 libgslcblas0
libgssapi-krb5-2 libhts-dev libhts3 libicu-dev libicu67 libk5crypto3
libkeyutils1 libklu1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmetis5
libmongoose2 libncurses-dev libncurses5-dev libncurses6 libncursesw6
libnghttp2-14 libpipeline1 libpsl5 librbio2 librtmp1 libruby2.7 libsigsegv2
libsliplu1 libspqr2 libsqlite3-dev libssh2-1 libssl-dev libssl1.1
libstdc++-10-dev libstdc++6 libsub-override-perl libsuitesparse-dev
libsuitesparseconfig5 libtinfo6 libtool libubsan1 libuchardet0 libumfpack5
libxml2 libyaml-0-2 lzma-dev m4 man-db openssl po-debconf rake ruby
ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert
ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales
dh-make gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev groff
libbamtools-doc liblapack-doc libboost1.71-doc libboost-atomic1.71-dev
libboost-chrono1.71-dev libboost-container1.71-dev libboost-context1.71-dev
libboost-contract1.71-dev libboost-coroutine1.71-dev
libboost-date-time1.71-dev libboost-exception1.71-dev libboost-fiber1.71-dev
libboost-filesystem1.71-dev libboost-graph1.71-dev
libboost-graph-parallel1.71-dev libboost-locale1.71-dev libboost-log1.71-dev
libboost-math1.71-dev libboost-mpi1.71-dev libboost-mpi-python1.71-dev
libboost-numpy1.71-dev libboost-program-options1.71-dev
libboost-python1.71-dev libboost-random1.71-dev
libboost-serialization1.71-dev libboost-stacktrace1.71-dev
libboost-system1.71-dev libboost-test1.71-dev libboost-thread1.71-dev
libboost-timer1.71-dev libboost-type-erasure1.71-dev libboost-wave1.71-dev
libboost1.71-tools-dev libmpfrc++-dev libntl-dev libcurl4-doc
libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev librtmp-dev
libssh2-1-dev pkg-config gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html krb5-doc krb5-user icu-doc liblzma-doc ncurses-doc
sqlite3-doc libssl-doc libstdc++-10-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl ri ruby-dev bundler
Recommended packages:
curl | wget | lynx bzip2-doc libarchive-cpio-perl libglib2.0-data
shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libltdl-dev
libmail-sendmail-perl zip fonts-lato libjs-jquery
The following NEW packages will be installed:
asciidoctor autoconf automake autopoint autotools-dev ca-certificates
debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext
gettext-base groff-base icu-devtools intltool-debian libamd2
libarchive-zip-perl libbam-dev libbamtools-dev libbamtools2.5.1 libblas-dev
libblas3 libboost-iostreams-dev libboost-iostreams1.71-dev
libboost-regex1.71-dev libboost-regex1.71.0 libboost1.71-dev libbrotli1
libbtf1 libbz2-dev libcamd2 libccolamd2 libcholmod3 libcolamd2 libcroco3
libcurl3-gnutls libcurl4-gnutls-dev libcxsparse3 libdebhelper-perl
libdeflate-dev libdeflate0 libelf1 libfile-stripnondeterminism-perl
libgfortran5 libglib2.0-0 libgraphblas3 libgsl-dev libgsl25 libgslcblas0
libgssapi-krb5-2 libhts-dev libhts3 libicu-dev libicu67 libk5crypto3
libkeyutils1 libklu1 libkrb5-3 libkrb5support0 liblapack-dev liblapack3
libldl2 liblpsolve55-dev liblzma-dev libmagic-mgc libmagic1 libmetis5
libmongoose2 libncurses-dev libncurses5-dev libncurses6 libnghttp2-14
libpipeline1 libpsl5 librbio2 librtmp1 libruby2.7 libsigsegv2 libsliplu1
libspqr2 libsqlite3-dev libssh2-1 libssl-dev libssl1.1 libsub-override-perl
libsuitesparse-dev libsuitesparseconfig5 libtool libuchardet0 libumfpack5
libxml2 libyaml-0-2 lzma-dev m4 man-db openssl po-debconf rake ruby
ruby-asciidoctor ruby-minitest ruby-net-telnet ruby-power-assert
ruby-test-unit ruby-xmlrpc ruby2.7 rubygems-integration
sbuild-build-depends-augustus-dummy zlib1g-dev
The following packages will be upgraded:
binutils binutils-arm-linux-gnueabihf binutils-common cpp-10 g++-10 gcc-10
gcc-10-base libasan6 libatomic1 libbinutils libcc1-0 libctf0 libgcc-10-dev
libgcc-s1 libgomp1 libncursesw6 libstdc++-10-dev libstdc++6 libtinfo6
libubsan1
20 upgraded, 110 newly installed, 0 to remove and 17 not upgraded.
Need to get 107 MB/108 MB of archives.
After this operation, 517 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-UdlUwo/apt_archive ./ sbuild-build-depends-augustus-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.0-13+rpi1 [31.7 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libctf0 armhf 2.35.1-1+rpi1 [35.3 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf binutils-arm-linux-gnueabihf armhf 2.35.1-1+rpi1 [1707 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libbinutils armhf 2.35.1-1+rpi1 [314 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf binutils-common armhf 2.35.1-1+rpi1 [2214 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf binutils armhf 2.35.1-1+rpi1 [60.1 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.2.0-13+rpi1 [199 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.2.0-13+rpi1 [36.1 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.2.0-13+rpi1 [84.1 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.2.0-13+rpi1 [8180 B]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libasan6 armhf 10.2.0-13+rpi1 [301 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.2.0-13+rpi1 [115 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf g++-10 armhf 10.2.0-13+rpi1 [6792 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-10-dev armhf 10.2.0-13+rpi1 [1746 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libgcc-10-dev armhf 10.2.0-13+rpi1 [685 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf gcc-10 armhf 10.2.0-13+rpi1 [12.3 MB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf cpp-10 armhf 10.2.0-13+rpi1 [6249 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.2.0-13+rpi1 [409 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libtinfo6 armhf 6.2+20200918-1 [327 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libncursesw6 armhf 6.2+20200918-1 [105 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf openssl armhf 1.1.1g-1 [811 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf ca-certificates all 20200601 [158 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf rubygems-integration all 1.17.2 [6384 B]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf rake all 13.0.1-4 [84.7 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf ruby-minitest all 5.13.0-1 [57.3 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf ruby-net-telnet all 0.1.1-2 [12.5 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf ruby-power-assert all 1.1.7-1 [11.4 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf ruby-test-unit all 3.3.5-1 [85.3 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf ruby-xmlrpc all 0.3.0-2 [23.7 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libyaml-0-2 armhf 0.2.2-1 [40.0 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libruby2.7 armhf 2.7.1-4 [3819 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf ruby2.7 armhf 2.7.1-4 [670 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf ruby armhf 1:2.7+1 [11.5 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf ruby-asciidoctor all 2.0.10-2 [201 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf asciidoctor all 2.0.10-2 [77.7 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.181-1 [161 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.0-2 [1173 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6 [578 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf icu-devtools armhf 67.1-4 [172 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libsuitesparseconfig5 armhf 1:5.8.1+dfsg-2 [22.6 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libamd2 armhf 1:5.8.1+dfsg-2 [29.3 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libbam-dev armhf 0.1.19-4 [111 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libbamtools2.5.1 armhf 2.5.1+dfsg-7 [133 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libbamtools-dev armhf 2.5.1+dfsg-7 [180 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libboost1.71-dev armhf 1.71.0-6+b1 [9099 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.71.0 armhf 1.71.0-6+b1 [435 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libicu-dev armhf 67.1-4 [9248 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libboost-regex1.71-dev armhf 1.71.0-6+b1 [571 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.71-dev armhf 1.71.0-6+b1 [271 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams-dev armhf 1.71.0.3+b3 [4388 B]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2 [259 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libbtf1 armhf 1:5.8.1+dfsg-2 [23.2 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-4 [28.0 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libcamd2 armhf 1:5.8.1+dfsg-2 [29.8 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libccolamd2 armhf 1:5.8.1+dfsg-2 [30.5 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libcolamd2 armhf 1:5.8.1+dfsg-2 [27.4 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.0-13+rpi1 [231 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libmetis5 armhf 5.1.0.dfsg-7 [133 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libcholmod3 armhf 1:5.8.1+dfsg-2 [212 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-10+b3 [62.0 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-10+b3 [112 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-10+b3 [318 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-10+b3 [135 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.41.0-3 [63.0 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.1 [54.2 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.72.0-1 [297 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libcurl4-gnutls-dev armhf 7.72.0-1 [371 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libcxsparse3 armhf 1:5.8.1+dfsg-2 [51.6 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libdeflate-dev armhf 1.6-1 [40.8 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libgraphblas3 armhf 1:5.8.1+dfsg-2 [4826 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libgsl-dev armhf 2.6+dfsg-2 [950 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.11-2 [318 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.11-2 [4495 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libklu1 armhf 1:5.8.1+dfsg-2 [51.1 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libldl2 armhf 1:5.8.1+dfsg-2 [23.0 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libmongoose2 armhf 1:5.8.1+dfsg-2 [43.3 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libumfpack5 armhf 1:5.8.1+dfsg-2 [127 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf librbio2 armhf 1:5.8.1+dfsg-2 [31.9 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libspqr2 armhf 1:5.8.1+dfsg-2 [68.7 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libsliplu1 armhf 1:5.8.1+dfsg-2 [48.1 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libsuitesparse-dev armhf 1:5.8.1+dfsg-2 [5224 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf liblpsolve55-dev armhf 5.5.2.5-2 [349 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20200918-1 [79.5 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libncurses-dev armhf 6.2+20200918-1 [290 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libncurses5-dev armhf 6.2+20200918-1 [940 B]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libsqlite3-dev armhf 3.33.0-1 [847 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf libssl-dev armhf 1.1.1g-1 [1573 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf lzma-dev all 9.22-2.1 [44.7 kB]
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Unpacking libbtf1:armhf (1:5.8.1+dfsg-2) ...
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Selecting previously unselected package libcamd2:armhf.
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Unpacking libcamd2:armhf (1:5.8.1+dfsg-2) ...
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Unpacking libmetis5:armhf (5.1.0.dfsg-7) ...
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Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
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Selecting previously unselected package libcxsparse3:armhf.
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Unpacking libdeflate-dev:armhf (1.6-1) ...
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Unpacking libhts-dev:armhf (1.11-2) ...
Selecting previously unselected package libklu1:armhf.
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Selecting previously unselected package liblapack-dev:armhf.
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Unpacking liblapack-dev:armhf (3.9.0-3) ...
Selecting previously unselected package libldl2:armhf.
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Unpacking libldl2:armhf (1:5.8.1+dfsg-2) ...
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Selecting previously unselected package librbio2:armhf.
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Unpacking librbio2:armhf (1:5.8.1+dfsg-2) ...
Selecting previously unselected package libspqr2:armhf.
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Unpacking libspqr2:armhf (1:5.8.1+dfsg-2) ...
Selecting previously unselected package libsliplu1:armhf.
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Selecting previously unselected package liblpsolve55-dev.
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Unpacking liblpsolve55-dev (5.5.2.5-2) ...
Selecting previously unselected package libncurses6:armhf.
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Unpacking libncurses6:armhf (6.2+20200918-1) ...
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Unpacking libncurses5-dev:armhf (6.2+20200918-1) ...
Selecting previously unselected package libsqlite3-dev:armhf.
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Unpacking libsqlite3-dev:armhf (3.33.0-1) ...
Selecting previously unselected package libssl-dev:armhf.
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Selecting previously unselected package lzma-dev.
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Unpacking sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libkeyutils1:armhf (1.6.1-2) ...
Setting up libpsl5:armhf (0.21.0-1.1) ...
Setting up libicu67:armhf (67.1-4) ...
Setting up libgslcblas0:armhf (2.6+dfsg-2) ...
Setting up ruby-power-assert (1.1.7-1) ...
Setting up libmagic-mgc (1:5.38-5) ...
Setting up libgsl25:armhf (2.6+dfsg-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libyaml-0-2:armhf (0.2.2-1) ...
Setting up libglib2.0-0:armhf (2.66.0-2) ...
No schema files found: doing nothing.
Setting up libssl1.1:armhf (1.1.1g-1) ...
Setting up libdebhelper-perl (13.2.1) ...
Setting up libbrotli1:armhf (1.0.9-2) ...
Setting up binutils-common:armhf (2.35.1-1+rpi1) ...
Setting up libldl2:armhf (1:5.8.1+dfsg-2) ...
Setting up libnghttp2-14:armhf (1.41.0-3) ...
Setting up libmagic1:armhf (1:5.38-5) ...
Setting up libdeflate0:armhf (1.6-1) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up libmetis5:armhf (5.1.0.dfsg-7) ...
Setting up file (1:5.38-5) ...
Setting up libgomp1:armhf (10.2.0-13+rpi1) ...
Setting up libbtf1:armhf (1:5.8.1+dfsg-2) ...
Setting up libasan6:armhf (10.2.0-13+rpi1) ...
Setting up libkrb5support0:armhf (1.17-10+b3) ...
Setting up ruby-minitest (5.13.0-1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libsqlite3-dev:armhf (3.33.0-1) ...
Setting up ruby-test-unit (3.3.5-1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20200918-1) ...
Setting up ruby-net-telnet (0.1.1-2) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libbamtools2.5.1:armhf (2.5.1+dfsg-7) ...
Setting up libssl-dev:armhf (1.1.1g-1) ...
Setting up libatomic1:armhf (10.2.0-13+rpi1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up icu-devtools (67.1-4) ...
Setting up libboost-regex1.71.0:armhf (1.71.0-6+b1) ...
Setting up libbam-dev (0.1.19-4) ...
Setting up libk5crypto3:armhf (1.17-10+b3) ...
Setting up libgfortran5:armhf (10.2.0-13+rpi1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up libubsan1:armhf (10.2.0-13+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libcxsparse3:armhf (1:5.8.1+dfsg-2) ...
Setting up libkrb5-3:armhf (1.17-10+b3) ...
Setting up libbinutils:armhf (2.35.1-1+rpi1) ...
Setting up openssl (1.1.1g-1) ...
Setting up libdeflate-dev:armhf (1.6-1) ...
Setting up libelf1:armhf (0.181-1) ...
Setting up libicu-dev:armhf (67.1-4) ...
Setting up ruby-xmlrpc (0.3.0-2) ...
Setting up libxml2:armhf (2.9.10+dfsg-6) ...
Setting up libsuitesparseconfig5:armhf (1:5.8.1+dfsg-2) ...
Setting up libcc1-0:armhf (10.2.0-13+rpi1) ...
Setting up cpp-10 (10.2.0-13+rpi1) ...
Setting up libblas-dev:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up librbio2:armhf (1:5.8.1+dfsg-2) ...
Setting up libbz2-dev:armhf (1.0.8-4) ...
Setting up libctf0:armhf (2.35.1-1+rpi1) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libamd2:armhf (1:5.8.1+dfsg-2) ...
Setting up libgraphblas3:armhf (1:5.8.1+dfsg-2) ...
Setting up liblapack3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libncurses-dev:armhf (6.2+20200918-1) ...
Setting up libgsl-dev (2.6+dfsg-2) ...
Setting up libcolamd2:armhf (1:5.8.1+dfsg-2) ...
Setting up libtool (2.4.6-14) ...
Setting up libgcc-10-dev:armhf (10.2.0-13+rpi1) ...
Setting up m4 (1.4.18-4) ...
Setting up libsliplu1:armhf (1:5.8.1+dfsg-2) ...
Setting up ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
126 added, 0 removed; done.
Setting up libcamd2:armhf (1:5.8.1+dfsg-2) ...
Setting up libmongoose2:armhf (1:5.8.1+dfsg-2) ...
Setting up libbamtools-dev:armhf (2.5.1+dfsg-7) ...
Setting up liblapack-dev:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-10+b3) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up lzma-dev (9.22-2.1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up libklu1:armhf (1:5.8.1+dfsg-2) ...
Setting up libccolamd2:armhf (1:5.8.1+dfsg-2) ...
Setting up libncurses5-dev:armhf (6.2+20200918-1) ...
Setting up binutils-arm-linux-gnueabihf (2.35.1-1+rpi1) ...
Setting up libcholmod3:armhf (1:5.8.1+dfsg-2) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libspqr2:armhf (1:5.8.1+dfsg-2) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libstdc++-10-dev:armhf (10.2.0-13+rpi1) ...
Setting up libboost1.71-dev:armhf (1.71.0-6+b1) ...
Setting up libcurl3-gnutls:armhf (7.72.0-1) ...
Setting up rubygems-integration (1.17.2) ...
Setting up binutils (2.35.1-1+rpi1) ...
Setting up libcurl4-gnutls-dev:armhf (7.72.0-1) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libumfpack5:armhf (1:5.8.1+dfsg-2) ...
Setting up libboost-regex1.71-dev:armhf (1.71.0-6+b1) ...
Setting up gcc-10 (10.2.0-13+rpi1) ...
Setting up libboost-iostreams1.71-dev:armhf (1.71.0-6+b1) ...
Setting up libhts3:armhf (1.11-2) ...
Setting up g++-10 (10.2.0-13+rpi1) ...
Setting up libsuitesparse-dev:armhf (1:5.8.1+dfsg-2) ...
Setting up po-debconf (1.0.21) ...
Setting up libhts-dev:armhf (1.11-2) ...
Setting up libboost-iostreams-dev:armhf (1.71.0.3+b3) ...
Setting up liblpsolve55-dev (5.5.2.5-2) ...
Setting up dh-autoreconf (19) ...
Setting up ruby2.7 (2.7.1-4) ...
Setting up debhelper (13.2.1) ...
Setting up ruby (1:2.7+1) ...
Setting up ruby-asciidoctor (2.0.10-2) ...
Setting up rake (13.0.1-4) ...
Setting up asciidoctor (2.0.10-2) ...
Setting up libruby2.7:armhf (2.7.1-4) ...
Setting up sbuild-build-depends-augustus-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-3+rpi1) ...
Processing triggers for ca-certificates (20200601) ...
Updating certificates in /etc/ssl/certs...
0 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d...
done.
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-1+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-13+rpi1 gcc-10_10.2.0-13+rpi1 libc6-dev_2.31-3+rpi1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 asciidoctor_2.0.10-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-7 binutils_2.35.1-1+rpi1 binutils-arm-linux-gnueabihf_2.35.1-1+rpi1 binutils-common_2.35.1-1+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 ca-certificates_20200601 coreutils_8.30-3 cpp_4:10.1.0-1+rpi1 cpp-10_10.2.0-13+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 g++_4:10.1.0-1+rpi1 g++-10_10.2.0-13+rpi1 gcc_4:10.1.0-1+rpi1 gcc-10_10.2.0-13+rpi1 gcc-10-base_10.2.0-13+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1+b1 gcc-8-base_8.4.0-4+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 icu-devtools_67.1-4 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 libacl1_2.2.53-8 libamd2_1:5.8.1+dfsg-2 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-13+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-13+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbam-dev_0.1.19-4 libbamtools-dev_2.5.1+dfsg-7 libbamtools2.5.1_2.5.1+dfsg-7 libbinutils_2.35.1-1+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36-3 libboost-iostreams-dev_1.71.0.3+b3 libboost-iostreams1.71-dev_1.71.0-6+b1 libboost-iostreams1.71.0_1.71.0-6+b1 libboost-regex1.71-dev_1.71.0-6+b1 libboost-regex1.71.0_1.71.0-6+b1 libboost1.71-dev_1.71.0-6+b1 libbrotli1_1.0.9-2 libbtf1_1:5.8.1+dfsg-2 libbz2-1.0_1.0.8-4 libbz2-dev_1.0.8-4 libc-bin_2.31-3+rpi1 libc-dev-bin_2.31-3+rpi1 libc6_2.31-3+rpi1 libc6-dev_2.31-3+rpi1 libcamd2_1:5.8.1+dfsg-2 libcap-ng0_0.7.9-2.2 libcap2_1:2.43-1 libcap2-bin_1:2.43-1 libcc1-0_10.2.0-13+rpi1 libccolamd2_1:5.8.1+dfsg-2 libcholmod3_1:5.8.1+dfsg-2 libcolamd2_1:5.8.1+dfsg-2 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35-2+rpi1 libctf0_2.35.1-1+rpi1 libcurl3-gnutls_7.72.0-1 libcurl4-gnutls-dev_7.72.0-1 libcwidget4_0.5.18-5 libcxsparse3_1:5.8.1+dfsg-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2.1 libdeflate-dev_1.6-1 libdeflate0_1.6-1 libdpkg-perl_1.20.5+rpi1 libelf1_0.181-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-10-dev_10.2.0-13+rpi1 libgcc-s1_10.2.0-13+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran5_10.2.0-13+rpi1 libglib2.0-0_2.66.0-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.2.0-13+rpi1 libgpg-error0_1.38-2 libgraphblas3_1:5.8.1+dfsg-2 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libhts-dev_1.11-2 libhts3_1.11-2 libicu-dev_67.1-4 libicu67_67.1-4 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libklu1_1:5.8.1+dfsg-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.51+dfsg-1 libldap-common_2.4.51+dfsg-1 libldl2_1:5.8.1+dfsg-2 liblocale-gettext-perl_1.07-4 liblpsolve55-dev_5.5.2.5-2 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmetis5_5.1.0.dfsg-7 libmongoose2_1:5.8.1+dfsg-2 libmount1_2.36-3 libmpc3_1.2.0~rc1-1 libmpfr6_4.1.0-3 libncurses-dev_6.2+20200918-1 libncurses5-dev_6.2+20200918-1 libncurses6_6.2+20200918-1 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnghttp2-14_1.41.0-3 libnpth0_1.6-2 libp11-kit0_0.23.21-2 libpam-cap_1:2.43-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.1 librbio2_1:5.8.1+dfsg-2 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libruby2.7_2.7.1-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsliplu1_1:5.8.1+dfsg-2 libsmartcols1_2.36-3 libspqr2_1:5.8.1+dfsg-2 libsqlite3-0_3.33.0-1 libsqlite3-dev_3.33.0-1 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl-dev_1.1.1g-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-13+rpi1 libstdc++6_10.2.0-13+rpi1 libsub-override-perl_0.09-2 libsuitesparse-dev_1:5.8.1+dfsg-2 libsuitesparseconfig5_1:5.8.1+dfsg-2 libsystemd0_246.2-1+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2+20200918-1 libtool_2.4.6-14 libubsan1_10.2.0-13+rpi1 libuchardet0_0.0.7-1 libudev1_246.2-1+rpi1 libumfpack5_1:5.8.1+dfsg-2 libunistring2_0.9.10-4 libuuid1_2.36-3 libxapian30_1.4.17-1 libxml2_2.9.10+dfsg-6 libyaml-0-2_0.2.2-1 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 lzma-dev_9.22-2.1 m4_1.4.18-4 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-3 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 openssl_1.1.1g-1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 rake_13.0.1-4 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 ruby_1:2.7+1 ruby-asciidoctor_2.0.10-2 ruby-minitest_5.13.0-1 ruby-net-telnet_0.1.1-2 ruby-power-assert_1.1.7-1 ruby-test-unit_3.3.5-1 ruby-xmlrpc_0.3.0-2 ruby2.7_2.7.1-4 rubygems-integration_1.17.2 sbuild-build-depends-augustus-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-4 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-3 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.WDVgF2Lw/trustedkeys.kbx': General error
gpgv: Signature made Wed Oct 7 12:05:21 2020 UTC
gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./augustus_3.3.3+dfsg-4.dsc
dpkg-source: info: extracting augustus in /<<BUILDDIR>>/augustus-3.3.3+dfsg
dpkg-source: info: unpacking augustus_3.3.3+dfsg.orig.tar.xz
dpkg-source: info: unpacking augustus_3.3.3+dfsg-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
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 interpreter_paths.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-06871c0d-0a82-4200-8c51-97de124468aa
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package augustus
dpkg-buildpackage: info: source version 3.3.3+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
/usr/bin/make -C auxprogs/bam2hints clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2hints'
rm -f bam2hints.o bam2hints ../../bin/bam2hints
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/homGeneMapping clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping'
(cd src; make clean; cd ../bin; rm -f homGeneMapping; cd ../../../bin; rm -f homGeneMapping)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src'
rm -f homGeneMapping gene.o genome.o
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src'
/bin/sh: 1: cd: can't cd to ../bin
/bin/sh: 1: cd: can't cd to ../../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping'
/usr/bin/make -C auxprogs/joingenes clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/joingenes'
rm -rf *o joingenes; rm -rf ../../bin/joingenes
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/joingenes'
/usr/bin/make -C auxprogs/aln2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/aln2wig'
rm -f aln2wig aln2wig.o; rm -f ../../bin/aln2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2wig clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2wig'
rm -f bam2wig bam2wig.o
rm -f ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/checkTargetSortedness'
rm -f *.o checkTargetSortedness
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands'
rm -f compileSpliceCands compileSpliceCands.o ../../bin/compileSpliceCands list.o
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam clean
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam'
(cd src; make clean;)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam/src'
rm -f *~ filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o
rm -f ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam'
rm -rf bin
rm -f debian/*substvars
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
mkdir -p bin
/usr/bin/make -C auxprogs/aln2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/aln2wig'
gcc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -c aln2wig.c
In file included from /usr/include/string.h:495,
from aln2wig.c:15:
In function 'strncpy',
inlined from 'main' at aln2wig.c:454:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'main' at aln2wig.c:460:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'main' at aln2wig.c:327:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'strncpy',
inlined from 'main' at aln2wig.c:334:6:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' output may be truncated copying 4095 bytes from a string of length 4095 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -Wall -Wno-sign-compare -ansi -pedantic -O2 -ggdb -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o aln2wig aln2wig.o;
cp aln2wig ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/aln2wig'
/usr/bin/make -C auxprogs/bam2hints
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2hints'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -o bam2hints bam2hints.o -lbamtools -lz
mkdir -p ../../bin
cp bam2hints ../../bin
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2hints'
/usr/bin/make -C auxprogs/bam2wig
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2wig'
cc -Wall -O2 -I/usr/include/samtools -I. -I/usr/include/htslib -I/usr/include/bcftools -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c bam2wig.c -o bam2wig.o
cc -Wall -O2 -I/usr/include/samtools -I. -I/usr/include/htslib -I/usr/include/bcftools -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now bam2wig.o -o bam2wig /usr/lib/libbam.a -lhts -lcurses -lm -lz -lpthread -lcurl -lssl -lcrypto -lbz2 -llzma
mkdir -p ../../bin
cp bam2wig ../../bin/bam2wig
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2wig'
/usr/bin/make -C auxprogs/checkTargetSortedness
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/checkTargetSortedness'
cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -c checkTargetSortedness.c -o checkTargetSortedness.o -I/usr/include/samtools -I.
cc -g -Wall -O2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now checkTargetSortedness.o -o checkTargetSortedness -lbam -lcurses -lm -lz -lpthread
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/checkTargetSortedness'
/usr/bin/make -C auxprogs/compileSpliceCands
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands'
cc -Wall -pedantic -ansi -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c compileSpliceCands.c
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:226:2: warning: this decimal constant is unsigned only in ISO C90
226 | s = malloc(3500000000);
| ^
In file included from /usr/include/string.h:495,
from compileSpliceCands.c:12:
In function 'strncat',
inlined from 'getChromosome' at compileSpliceCands.c:216:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:136:10: warning: '__builtin_strncat' specified bound depends on the length of the source argument [-Wstringop-overflow=]
136 | return __builtin___strncat_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c: In function 'getChromosome':
compileSpliceCands.c:216:2: note: length computed here
216 | strncat(checkstring,chromosomename,strlen(chromosomename));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c:226:6: warning: argument 1 value '3500000000' exceeds maximum object size 2147483647 [-Walloc-size-larger-than=]
226 | s = malloc(3500000000);
| ^~~~~~~~~~~~~~~~~~
In file included from compileSpliceCands.c:14:
/usr/include/stdlib.h:539:14: note: in a call to allocation function 'malloc' declared here
539 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
| ^~~~~~
In file included from /usr/include/string.h:495,
from compileSpliceCands.c:12:
In function 'strncpy',
inlined from 'parseLine' at compileSpliceCands.c:292:2:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:10: warning: '__builtin_strncpy' specified bound 256 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compileSpliceCands.c: In function 'parseList':
compileSpliceCands.c:350:36: warning: 'left' may be used uninitialized in this function [-Wmaybe-uninitialized]
350 | 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]
563 | parseList(&L,actualChromosome,chromosomeLength,oldname,maxSpliceSiteDiff,threshold,maxIntronLength);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c -o list.o list.c
cc -o compileSpliceCands compileSpliceCands.o list.o -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now;
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands'
/usr/bin/make -C auxprogs/filterBam
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam'
(cd src;make)
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filterBam.cc -o filterBam.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/MatePairs.cc -o MatePairs.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/getReferenceName.cc -o getReferenceName.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/initOptions.cc -o initOptions.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/SingleAlignment.cc -o SingleAlignment.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/printElapsedTime.cc -o printElapsedTime.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumMandIOperations.cc -o sumMandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/sumDandIOperations.cc -o sumDandIOperations.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c functions/PairednessCoverage.cc -o PairednessCoverage.o -I/usr/include/bamtools -Iheaders -I./bamtools
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
mv filterBam ../../../bin/filterBam
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam/src'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam'
/usr/bin/make -C auxprogs/homGeneMapping/src
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src'
g++ -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -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-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -Wno-sign-compare -ansi -pedantic -std=c++0x -pthread -o homGeneMapping main.cc gene.o genome.o -I../include
mkdir -p ../../../bin/
cp homGeneMapping ../../../bin/homGeneMapping
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src'
/usr/bin/make -C auxprogs/joingenes
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/joingenes'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_transcript.cpp
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x jg_ios.cpp
In file included from /usr/include/string.h:495,
from jg_transcript.h:5,
from jg_ios.cpp:1:
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'void load(std::unordered_map<std::__cxx11::basic_string<char>, Gene*>&, std::string&, int&, std::unordered_map<std::__cxx11::basic_string<char>, bool>&, Properties&)' at jg_ios.cpp:251:14:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'void load(std::unordered_map<std::__cxx11::basic_string<char>, Gene*>&, std::string&, int&, std::unordered_map<std::__cxx11::basic_string<char>, bool>&, Properties&)' at jg_ios.cpp:79:14:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'void load(std::unordered_map<std::__cxx11::basic_string<char>, Gene*>&, std::string&, int&, std::unordered_map<std::__cxx11::basic_string<char>, bool>&, Properties&)' at jg_ios.cpp:148:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' specified bound 300 equals destination size [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -std=gnu++0x joingenes.o jg_transcript.o jg_ios.o -o joingenes -Wl,-z,relro -Wl,-z,now
cp joingenes ../../bin/
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/joingenes'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
mkdir -p bin
cd src && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/src'
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_hitseq.o pp_hitseq.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_scoring.o pp_scoring.cc -I../include
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PP::Column&}; _Tp = PP::Column; _Alloc = std::allocator<PP::Column>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PP::Column>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:20,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'PP::Block::Block(PP::DistanceType, const std::vector<std::__cxx11::basic_string<char> >&, std::string)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Column*, std::vector<PP::Column> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'bool PP::Block::_ZN2PP5Block14initThresholdsEv.part.0()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:20,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {PP::Block}; _Tp = PP::Block; _Alloc = std::allocator<PP::Block>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PP::Block>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void PP::Profile::parse_stream(std::istream&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::Block*, std::vector<PP::Block> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o statemodel.o statemodel.cc -I../include
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, LLDouble>; _KeyOfValue = std::_Select1st<std::pair<const int, LLDouble> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/10/bits/stl_tree.h:2458:7: 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' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o namgene.o namgene.cc -I../include
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:20,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/stl_vector.h: In member function 'bool PP::BlockScoreType::addBlocksUntil(bool, int, std::map<int, LLDouble>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/geneticcode.hh:12,
from ../include/pp_profile.hh:16,
from pp_profile.cc:11:
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o types.o types.cc -I../include
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const PP::BonusProbEntry&}; _Tp = PP::BonusProbEntry; _Alloc = std::allocator<PP::BonusProbEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<PP::BonusProbEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/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++/10/bits/stl_tree.h:2524:5: 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' changed in GCC 7.1
2524 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2524:5: 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' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:20,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void PP::MultiTargetExonScorer::initBonusProbs(PP::BonusProbType&, int, int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<PP::BonusProbEntry*, std::vector<PP::BonusProbEntry> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/10/bits/stl_tree.h:2193:5: 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' changed in GCC 7.1
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In member function 'void PP::SubstateModel::scoreAssOrRDss(ViterbiSubmapType&, bool, int, const Double&)':
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SubstateId&>, std::tuple<>}; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/10/bits/stl_tree.h:2458:7: 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' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In member function 'void PP::SubstateModel::clearLowScoring(ViterbiSubmapType&)':
/usr/include/c++/10/bits/stl_tree.h:2542:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h:2542:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h:2542:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h:2542:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h:2542:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from types.cc:8:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from types.cc:8:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::postProcessing(const Double&)':
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from types.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h: In member function 'virtual void PP::SingleTargetExonScorer::exportSubstates(ViterbiSubmapType&)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In member function 'void PP::MultiTargetExonScorer::updateBonusProbs(PP::Position, const Double&)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void Constant::init()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'virtual void PP::MultiTargetExonScorer::scoreInternal(ViterbiColumnType&, int, const Double&)':
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/pp_scoring.hh:16,
from pp_scoring.cc:10:
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from types.cc:8:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1662 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1937 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'Double quantile(const std::vector<LLDouble>&, float)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from statemodel.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Ancestor}; _Tp = Ancestor; _Alloc = std::allocator<Ancestor>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Ancestor>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void StateModel::initPredecessors(Matrix<LLDouble>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Ancestor*, std::vector<Ancestor> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o gene.o gene.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o motif.o motif.cc -I../include
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from motif.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from motif.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In member function 'Double Motif::getProbThreshold(double, int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o geneticcode.o geneticcode.cc -I../include
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from ../include/geneticcode.hh:12,
from ../include/motif.hh:13,
from ../include/gene.hh:12,
from gene.cc:8:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from ../include/geneticcode.hh:12,
from ../include/motif.hh:13,
from ../include/gene.hh:12,
from gene.cc:8:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o projectio.o projectio.cc -I../include
In file included from /usr/include/string.h:495,
from /usr/include/c++/10/cstring:42,
from ../include/types.hh:18,
from ../include/hints.hh:12,
from hints.cc:10:
In function 'char* strncpy(char*, const char*, size_t)',
inlined from 'std::istream& operator>>(std::istream&, Feature&)' at hints.cc:82:9:
/usr/include/arm-linux-gnueabihf/bits/string_fortified.h:106:34: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output may be truncated copying 1014 bytes from a string of length 1023 [-Wstringop-truncation]
106 | return __builtin___strncpy_chk (__dest, __src, __len, __bos (__dest));
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exonmodel.o exonmodel.cc -I../include
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from ../include/gene.hh:12,
from gene.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void examineBaseCountOfGeneSeq(AnnoSequence*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from ../include/geneticcode.hh:12,
from ../include/motif.hh:13,
from ../include/gene.hh:12,
from gene.cc:8:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/list:64,
from ../include/vitmatrix.hh:17,
from ../include/pp_scoring.hh:16,
from ../include/gene.hh:13,
from gene.cc:8:
/usr/include/c++/10/bits/list.tcc: In member function 'std::__cxx11::list<_Tp, _Alloc>::iterator std::__cxx11::list<_Tp, _Alloc>::insert(std::__cxx11::list<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = std::_List_const_iterator<PP::Match>; <template-parameter-2-2> = void; _Tp = PP::Match; _Alloc = std::allocator<PP::Match>]':
/usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::__cxx11::list<PP::Match>::const_iterator' changed in GCC 7.1
133 | list<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/10/bits/list.tcc:133:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/10/bits/list.tcc: In 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++/10/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
308 | list<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/list.tcc:308:7: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/10/bits/list.tcc:320:17: note: parameter passing for argument of type 'std::__cxx11::list<PP::Match>::const_iterator' changed in GCC 7.1
320 | insert(__last1, __first2, __last2);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/list.tcc:320:17: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
/usr/include/c++/10/bits/list.tcc: In static member function 'static StatePath* StatePath::condenseStatePath(StatePath*)':
/usr/include/c++/10/bits/list.tcc:286:22: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/list.tcc: In copy constructor 'Gene::Gene(const Gene&)':
/usr/include/c++/10/bits/list.tcc:286:22: note: parameter passing for argument of type 'std::_List_const_iterator<PP::Match>' changed in GCC 7.1
286 | _M_assign_dispatch(__x.begin(), __x.end(), __false_type());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenicmodel.o igenicmodel.cc -I../include
exonmodel.cc: In static member function 'static void ExonModel::readAllParameters()':
exonmodel.cc:671:28: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
671 | sprintf(zusString, "[%d]", idx+1);
| ^~
exonmodel.cc:671:26: note: directive argument in the range [1, 2147483647]
671 | sprintf(zusString, "[%d]", idx+1);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /usr/include/c++/10/cstdio:42,
from /usr/include/c++/10/ext/string_conversions.h:43,
from /usr/include/c++/10/bits/basic_string.h:6535,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/ios:42,
from /usr/include/c++/10/ostream:38,
from ../include/matrix.hh:13,
from ../include/statemodel.hh:12,
from ../include/exonmodel.hh:11,
from exonmodel.cc:8:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/statemodel.hh:13,
from ../include/intronmodel.hh:11,
from intronmodel.cc:8:
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, LLDouble>; _KeyOfValue = std::_Select1st<std::pair<const int, LLDouble> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, LLDouble> >]':
/usr/include/c++/10/bits/stl_tree.h:2458:7: 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' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from ../include/statemodel.hh:13,
from ../include/intronmodel.hh:11,
from intronmodel.cc:8:
/usr/include/c++/10/bits/stl_map.h: In static member function 'static Double IntronModel::dSSProb(int, bool)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h: In static member function 'static Double IntronModel::aSSProb(int, bool)':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o merkmal.o merkmal.cc -I../include
igenicmodel.cc: In static member function 'static void IGenicModel::readAllParameters()':
igenicmodel.cc:162:25: warning: '%d' directive writing between 1 and 10 bytes into a region of size 5 [-Wformat-overflow=]
162 | sprintf(zusString, "[%d]", idx+1);
| ^~
igenicmodel.cc:162:23: note: directive argument in the range [1, 2147483647]
162 | sprintf(zusString, "[%d]", idx+1);
| ^~~~~~
In file included from /usr/include/stdio.h:867,
from /usr/include/c++/10/cstdio:42,
from /usr/include/c++/10/ext/string_conversions.h:43,
from /usr/include/c++/10/bits/basic_string.h:6535,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/ios:42,
from /usr/include/c++/10/ostream:38,
from ../include/matrix.hh:13,
from ../include/statemodel.hh:12,
from ../include/igenicmodel.hh:11,
from igenicmodel.cc:10:
/usr/include/arm-linux-gnueabihf/bits/stdio2.h:36:34: note: '__builtin___sprintf_chk' output between 4 and 13 bytes into a destination of size 6
36 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
37 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/hints.hh:12,
from ../include/extrinsicinfo.hh:15,
from extrinsicinfo.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = Feature; _Val = Feature; _KeyOfValue = std::_Identity<Feature>; _Compare = std::less<Feature>; _Alloc = std::allocator<Feature>]':
/usr/include/c++/10/bits/stl_tree.h:2193:5: note: parameter passing for argument of type 'std::_Rb_tree<Feature, Feature, std::_Identity<Feature>, std::less<Feature>, std::allocator<Feature> >::const_iterator' changed in GCC 7.1
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from ../include/hints.hh:12,
from ../include/extrinsicinfo.hh:15,
from extrinsicinfo.cc:10:
/usr/include/c++/10/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++/10/bits/stl_algo.h:5368:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5368 | __set_difference(_InputIterator1 __first1, _InputIterator1 __last1,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5368:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5368:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5368:5: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o vitmatrix.o vitmatrix.cc -I../include
/usr/include/c++/10/bits/stl_algo.h: In member function 'void FeatureCollection::printAccuracyForSequenceSet(const AnnoSequence*, bool)':
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
5433 | return _GLIBCXX_STD_A::__set_difference(__first1, __last1,
| ^
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5433:46: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator<Feature>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const ViterbiSubmapType&}; _Tp = ViterbiSubmapType; _Alloc = std::allocator<ViterbiSubmapType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ViterbiSubmapType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/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++/10/bits/stl_tree.h:2524:5: 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' changed in GCC 7.1
2524 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:2524:5: 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' changed in GCC 7.1
/usr/include/c++/10/bits/stl_tree.h: In member function 'void ViterbiSubmapType::useMaximum(Double&)':
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h:1245:14: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
1245 | _M_erase_aux(__first, __last);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In member function 'int ViterbiSubmapType::eraseUnneededSubstate(SubstateId)':
/usr/include/c++/10/bits/stl_tree.h:2542:19: note: parameter passing for argument of type 'std::_Rb_tree<SubstateId, std::pair<const SubstateId, ViterbiSubmapEntry>, std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >, std::less<SubstateId>, std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> > >::const_iterator' changed in GCC 7.1
2542 | _M_erase_aux(__p.first, __p.second);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {ViterbiEntryType}; _Tp = ViterbiEntryType; _Alloc = std::allocator<ViterbiEntryType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<ViterbiEntryType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void ViterbiColumnType::addState(int, signed char)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiEntryType*, std::vector<ViterbiEntryType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:20,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In member function 'ViterbiSubmapType& ViterbiColumnType::addSubstates(const ViterbiSubmapType&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<ViterbiSubmapType*, std::vector<ViterbiSubmapType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/map:60,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/10/bits/stl_tree.h:2193:5: 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' changed in GCC 7.1
2193 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const SubstateId&>, std::tuple<>}; _Key = SubstateId; _Val = std::pair<const SubstateId, ViterbiSubmapEntry>; _KeyOfValue = std::_Select1st<std::pair<const SubstateId, ViterbiSubmapEntry> >; _Compare = std::less<SubstateId>; _Alloc = std::allocator<std::pair<const SubstateId, ViterbiSubmapEntry> >]':
/usr/include/c++/10/bits/stl_tree.h:2458:7: 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' changed in GCC 7.1
2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/map:61,
from ../include/types.hh:23,
from ../include/vitmatrix.hh:12,
from vitmatrix.cc:10:
/usr/include/c++/10/bits/stl_map.h: In member function 'void ViterbiSubmapType::registerPredecessors()':
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_map.h:501:37: 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' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o lldouble.o lldouble.cc -I../include
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/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++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o mea.o mea.cc -I../include
/usr/include/c++/10/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++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In static member function 'static std::vector<double> CRF::capOutliers(std::vector<double>)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o graph.o graph.cc -I../include
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {LLDouble}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void Parameters::addMerkmal(Double*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:20,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/types.hh:20,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void CRF::onlineLargeMarginTraining(Parameters*, std::vector<AnnoSequence*>, FeatureCollection&)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/motif.hh:12,
from ../include/gene.hh:12,
from ../include/mea.hh:11,
from mea.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'AugustusGraph::AugustusGraph(std::__cxx11::list<Status>*, const char*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = int; V = double]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o meaPath.o meaPath.cc -I../include
In file included from /usr/include/c++/10/algorithm:62,
from ../include/types.hh:22,
from ../include/merkmal.hh:14,
from merkmal.cc:10:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1662 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1662:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o exoncand.o exoncand.cc -I../include
/usr/include/c++/10/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++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1937:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1937 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In member function 'void BinnedMMGroup::trainBins(int)':
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o igenictrain.o igenictrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o introntrain.o introntrain.cc -I../include
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/ncmodel.hh:11,
from ncmodel.cc:8:
/usr/include/c++/10/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++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/ncmodel.hh:11,
from ncmodel.cc:8:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void NcModel::computeLengthDistributions()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o utrtrain.o utrtrain.cc -I../include
g++ -c -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o dummy.o dummy.cc -I../include
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/intronmodel.hh:11,
from introntrain.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/intronmodel.hh:11,
from introntrain.cc:8:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void IntronModel::makeDSSProbs()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void IntronModel::buildProbabilities(const AnnoSequence*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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 -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc -I../include
In file included from /usr/include/c++/10/vector:72,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/exonmodel.hh:11,
from exontrain.cc:8:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const LLDouble&}; _Tp = LLDouble; _Alloc = std::allocator<LLDouble>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<LLDouble>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from ../include/matrix.hh:12,
from ../include/statemodel.hh:12,
from ../include/exonmodel.hh:11,
from exontrain.cc:8:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void ExonModel::buildProbabilities()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<LLDouble*, std::vector<LLDouble> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
echo "-Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security" > cxxflags
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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
cp prepareAlign ../bin/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+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
In file included from /usr/include/c++/10/vector:72,
from ../include/types.hh:20,
from etraining.cc:9:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void CRF::compareWeights(Parameters*, std::vector<T>&, std::vector<V>&, int) [with U = double; V = double]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cp augustus ../bin/
cp fastBlockSearch ../bin/
cp etraining ../bin/
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/src'
cd auxprogs && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs'
cd bam2hints; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+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-3.3.3+dfsg/auxprogs/bam2hints'
cd compileSpliceCands; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'compileSpliceCands' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands'
cd filterBam; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src;make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam/src'
g++ -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -std=c++0x -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now filterBam.o MatePairs.o getReferenceName.o initOptions.o SingleAlignment.o printElapsedTime.o sumMandIOperations.o sumDandIOperations.o PairednessCoverage.o -o filterBam -lbamtools -lz
filterBam compiled with BAMTOOLS=/usr/include/bamtools
mv filterBam ../../../bin/filterBam
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/filterBam'
cd homGeneMapping; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
(cd src; make)
make[5]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src'
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/homGeneMapping'
cd joingenes; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+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-3.3.3+dfsg/auxprogs/joingenes'
cd bam2wig; make;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2wig'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[4]: 'bam2wig' is up to date.
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/bam2wig'
cd utrrnaseq/Debug; make all;
make[4]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/Debug'
make[4]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
Building file: ../src/Compute_UTRs.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Compute_UTRs.d" -MT"src/Compute_UTRs.o" -o "src/Compute_UTRs.o" "../src/Compute_UTRs.cpp"
Finished building: ../src/Compute_UTRs.cpp
Building file: ../src/Coord_Transform.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Coord_Transform.d" -MT"src/Coord_Transform.o" -o "src/Coord_Transform.o" "../src/Coord_Transform.cpp"
Finished building: ../src/Coord_Transform.cpp
Building file: ../src/Genomic_Data.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Genomic_Data.d" -MT"src/Genomic_Data.o" -o "src/Genomic_Data.o" "../src/Genomic_Data.cpp"
Finished building: ../src/Genomic_Data.cpp
Building file: ../src/Splice_Sites.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Splice_Sites.d" -MT"src/Splice_Sites.o" -o "src/Splice_Sites.o" "../src/Splice_Sites.cpp"
Finished building: ../src/Splice_Sites.cpp
Building file: ../src/Supporting_Methods.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Supporting_Methods.d" -MT"src/Supporting_Methods.o" -o "src/Supporting_Methods.o" "../src/Supporting_Methods.cpp"
Finished building: ../src/Supporting_Methods.cpp
Building file: ../src/Test.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/Test.d" -MT"src/Test.o" -o "src/Test.o" "../src/Test.cpp"
Finished building: ../src/Test.cpp
Building file: ../src/UTRs.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/UTRs.d" -MT"src/UTRs.o" -o "src/UTRs.o" "../src/UTRs.cpp"
../src/UTRs.cpp: In static member function 'static void UTRs::compute_UTRs(const Genomic_Data::Scaff_plus_Gen_Data&, const std::map<unsigned int, double>&)':
../src/UTRs.cpp:387:64: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
387 | vector<double>::iterator jt = min_element(d.begin(), d.end());
| ^
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/core/swap.hpp:27,
from /usr/include/boost/utility/swap.hpp:15,
from /usr/include/boost/tuple/detail/tuple_basic.hpp:40,
from /usr/include/boost/tuple/tuple.hpp:28,
from ../src/Compute_UTRs.hpp:16,
from ../src/UTRs.cpp:9:
/usr/include/c++/10/bits/stl_algo.h: In function 'constexpr _FIter std::min_element(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]':
/usr/include/c++/10/bits/stl_algo.h:5651:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5651 | inline min_element(_ForwardIterator __first, _ForwardIterator __last)
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5651:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5660:43: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5660 | return _GLIBCXX_STD_A::__min_element(__first, __last,
| ^
In file included from /usr/include/c++/10/bits/stl_algobase.h:71,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/predefined_ops.h: In member function 'constexpr bool __gnu_cxx::__ops::_Iter_less_iter::operator()(_Iterator1, _Iterator2) const [with _Iterator1 = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Iterator2 = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >]':
/usr/include/c++/10/bits/predefined_ops.h:42:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
42 | operator()(_Iterator1 __it1, _Iterator2 __it2) const
| ^~~~~~~~
/usr/include/c++/10/bits/predefined_ops.h:42:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /usr/include/boost/core/swap.hpp:27,
from /usr/include/boost/utility/swap.hpp:15,
from /usr/include/boost/tuple/detail/tuple_basic.hpp:40,
from /usr/include/boost/tuple/tuple.hpp:28,
from ../src/Compute_UTRs.hpp:16,
from ../src/UTRs.cpp:9:
/usr/include/c++/10/bits/stl_algo.h: In function 'constexpr _ForwardIterator std::__min_element(_ForwardIterator, _ForwardIterator, _Compare) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/10/bits/stl_algo.h:5629:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5629 | __min_element(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:5629:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:5636:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
5636 | if (__comp(__first, __result))
| ~~~~~~^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from ../src/Genomic_Data.hpp:9,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator<double>]':
/usr/include/c++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
346 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
107 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:109:27: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
109 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
560 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algobase.h:67,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from ../src/Genomic_Data.hpp:8,
from ../src/UTRs.cpp:5:
/usr/include/c++/10/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]':
/usr/include/c++/10/bits/stl_iterator.h:2169:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
2169 | __miter_base(move_iterator<_Iterator> __it)
| ^~~~~~~~~~~~
Finished building: ../src/UTRs.cpp
Building file: ../src/main.cpp
Invoking: GCC C++ Compiler
g++ -I/usr/include/boost -O0 -g3 -pedantic -Wall -c -fmessage-length=0 -MMD -MP -MF"src/main.d" -MT"src/main.o" -o "src/main.o" "../src/main.cpp"
Finished building: ../src/main.cpp
Building target: utrrnaseq
Invoking: GCC C++ Linker
g++ -o "utrrnaseq" ./src/Compute_UTRs.o ./src/Coord_Transform.o ./src/Genomic_Data.o ./src/Splice_Sites.o ./src/Supporting_Methods.o ./src/Test.o ./src/UTRs.o ./src/main.o
Finished building target: utrrnaseq
make[4]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/Debug'
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/auxprogs'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
asciidoctor -a docdate='' -b manpage debian/mansrc/*adoc
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
dh_auto_test -a
make -j4 test
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
cd src && make unittest
make[2]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/src'
cd googletest && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/src/googletest'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -isystem ./include -I. -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wextra -pthread -std=c++11 -c \
./src/gtest-all.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -isystem ./include -I. -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wextra -pthread -std=c++11 -c \
./src/gtest_main.cc
ar rv libgtest.a gtest-all.o
ar rv libgtest_main.a gtest-all.o gtest_main.o
ar: ar: creating libgtest_main.a
creating libgtest.a
a - gtest-all.o
a - gtest-all.o
a - gtest_main.o
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/src/googletest'
cd unittests && make
make[3]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/src/unittests'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -pedantic -pthread -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -L../googletest -lgtest -lgtest_main -I../../include -isystem ../googletest/include/ -c lldouble_unittest.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -pedantic -pthread -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -L../googletest -lgtest -lgtest_main -I../../include -isystem ../googletest/include/ -c fasta_unittest.cc
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -pedantic -pthread -Wall -Wno-sign-compare -pedantic -g -ggdb -O3 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/augustus-3.3.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -L../googletest -lgtest -lgtest_main -I../../include -isystem ../googletest/include/ lldouble_unittest.o fasta_unittest.o ../lldouble.o ../fasta.o -o unittests
make[3]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/src/unittests'
make[2]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg/src'
cd src/unittests && ./unittests
Running main() from ./src/gtest_main.cc
[==========] Running 4 tests from 2 test suites.
[----------] Global test environment set-up.
[----------] 3 tests from LLDoubleTest
[ RUN ] LLDoubleTest.Summation
[ OK ] LLDoubleTest.Summation (0 ms)
[ RUN ] LLDoubleTest.SimpleMultiplication
[ OK ] LLDoubleTest.SimpleMultiplication (0 ms)
[ RUN ] LLDoubleTest.ChainMultiplication
[ OK ] LLDoubleTest.ChainMultiplication (1 ms)
[----------] 3 tests from LLDoubleTest (3 ms total)
[----------] 1 test from FastaTest
[ RUN ] FastaTest.ReadFile
[ OK ] FastaTest.ReadFile (0 ms)
[----------] 1 test from FastaTest (0 ms total)
[----------] Global test environment tear-down
[==========] 4 tests from 2 test suites ran. (3 ms total)
[ PASSED ] 4 tests.
./bin/augustus --species=human --UTR=on examples/example.fa
# This output was generated with AUGUSTUS (version 3.3.3).
# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
# O. Keller, S. König, L. Gerischer, L. Romoth and Katharina Hoff.
# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initializing the parameters using config directory /<<BUILDDIR>>/augustus-3.3.3+dfsg/config/ ...
# human version. Using species specific transition matrix: /<<BUILDDIR>>/augustus-3.3.3+dfsg/config/species/human/human_trans_shadow_partial_utr.pbl
# Looks like examples/example.fa is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
#
# Predicted genes for sequence number 1 on both strands
# start gene g1
HS04636 AUGUSTUS gene 836 8857 1 + . g1
HS04636 AUGUSTUS transcript 836 8857 . + . g1.t1
HS04636 AUGUSTUS tss 836 836 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 836 1017 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 1818 1934 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 2055 2198 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 2852 2995 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 3426 3607 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 4340 4423 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 4543 4789 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 5072 5358 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 5860 6007 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS exon 6494 8857 . + . transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "g1.t1"; gene_id "g1";
HS04636 AUGUSTUS tts 8857 8857 . + . transcript_id "g1.t1"; gene_id "g1";
# protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
# THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
# PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
# end gene g1
###
#
# ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
#
# Predicted genes for sequence number 2 on both strands
# start gene g2
HS08198 AUGUSTUS gene 86 2344 1 + . g2
HS08198 AUGUSTUS transcript 86 2344 . + . g2.t1
HS08198 AUGUSTUS tss 86 86 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 86 582 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 812 894 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1053 1123 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1208 1315 . + . transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2";
HS08198 AUGUSTUS exon 1587 1688 . + . transcript_id "g2.t1"; gene_id "g2";
# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY]
# end gene g2
###
# command line:
# ./bin/augustus --species=human --UTR=on examples/example.fa
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
mkdir -p debian/augustus/usr/bin
install bin/* debian/augustus/usr/bin
install auxprogs/checkTargetSortedness/checkTargetSortedness \
debian/augustus/usr/bin
install auxprogs/bam2wig/bam2wig \
debian/augustus/usr/bin
install auxprogs/compileSpliceCands/compileSpliceCands \
debian/augustus/usr/bin
install auxprogs/homGeneMapping/src/homGeneMapping \
debian/augustus/usr/bin
install auxprogs/joingenes/joingenes \
debian/augustus/usr/bin
mkdir -p debian/augustus/usr/share/augustus
cp -r scripts debian/augustus/usr/share/augustus
chmod -R -x debian/augustus/usr/share/augustus/scripts/*
rm -rf debian/augustus/usr/share/augustus/scripts/*.patch \
debian/augustus/usr/share/augustus/scripts/aln2wig
chmod +x debian/augustus/usr/share/augustus/scripts/checkUTR \
debian/augustus/usr/share/augustus/scripts/*.pl*
mkdir -p debian/augustus-doc/usr/share/doc/augustus
cp README* debian/augustus-doc/usr/share/doc/augustus
cp docs/*.txt debian/augustus-doc/usr/share/doc/augustus
cp -r docs/tutorial \
debian/augustus-doc/usr/share/doc/augustus
mkdir -p debian/augustus-data/usr/share/augustus
cp -r config debian/augustus-data/usr/share/augustus
find debian/augustus-data/usr/share/augustus \
-type f -exec chmod -x {} \;
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
dh_installchangelogs -k HISTORY.TXT
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
debian/rules override_dh_compress
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
dh_compress -Xtutorial
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
dh_fixperms -a
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -a
dpkg-shlibdeps: warning: debian/augustus/usr/bin/etraining contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/augustus/usr/bin/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/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/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/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/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/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/joingenes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a
debian/rules override_dh_gencontrol
make[1]: Entering directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
echo "libbam-dev:Version=0.1.19-4" >> debian/augustus.substvars
dh_gencontrol
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package augustus: substitution variable ${perl:Depends} unused, but is defined
make[1]: Leaving directory '/<<BUILDDIR>>/augustus-3.3.3+dfsg'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'augustus' in '../augustus_3.3.3+dfsg-4_armhf.deb'.
dpkg-deb: building package 'augustus-dbgsym' in '../augustus-dbgsym_3.3.3+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../augustus_3.3.3+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-10-09T05:35:14Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
augustus_3.3.3+dfsg-4_armhf.changes:
------------------------------------
Format: 1.8
Date: Wed, 07 Oct 2020 13:20:31 +0200
Source: augustus
Binary: augustus augustus-dbgsym
Architecture: armhf
Version: 3.3.3+dfsg-4
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Sascha Steinbiss <satta@debian.org>
Description:
augustus - gene prediction in eukaryotic genomes
Closes: 971792
Changes:
augustus (3.3.3+dfsg-4) unstable; urgency=medium
.
* Drop conflicting build-dep on libcurl4-nss-dev.
Closes: 971792
* Use debhelper 13.
* Add Rules-Requires-Root: no.
Checksums-Sha1:
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4c17fb607da45c3c5db28f0692b4cab2cab00a60 7374 augustus_3.3.3+dfsg-4_armhf.buildinfo
c77e778f18d6c5697debe91e8fa540326c594183 892480 augustus_3.3.3+dfsg-4_armhf.deb
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56b4688e22653eb47c1546dc68e15fe66715ef3e6dd7aebb6d5c82db0f4e1f5f 7374 augustus_3.3.3+dfsg-4_armhf.buildinfo
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Files:
cf0212f230afe5d207caacc93ac43cb4 15629712 debug optional augustus-dbgsym_3.3.3+dfsg-4_armhf.deb
c77ea4e06448d89e313bf30fcf222399 7374 science optional augustus_3.3.3+dfsg-4_armhf.buildinfo
ffde78269db9ed2231b2b912f2a40835 892480 science optional augustus_3.3.3+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
augustus-dbgsym_3.3.3+dfsg-4_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 15629712 bytes: control archive=1156 bytes.
837 bytes, 12 lines control
1360 bytes, 13 lines md5sums
Package: augustus-dbgsym
Source: augustus
Version: 3.3.3+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 15967
Depends: augustus (= 3.3.3+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for augustus
Build-Ids: 06d9ce7729891c0da8ba83050b8bf28c9e47e044 3bf2b7f153bb48dce5358d08b3a96005401102d6 471f1abd127f6fc238d03c9373403435dc4a4e26 484cf80b37dd6a680b0396ce83a0ba371d037651 5faf162a47690426da2211010d957c4dbc8d8dc9 69213aaddf21221363be65ab9cc7435352934c97 9dda9757f413a090b1c3aa724aa5c1220ee3ffe8 a9c83e566926bfbc1b33e2fe7e9adebcfdc76b55 aafa776fadeb97c818fc2dab53d69a9429ae8277 b7f9ea805b4b2850a709fe6d62a5ebbc6f54e5b5 bb4cb964cb6f226cc7141512ad592a80530abe11 e4ae26f66f0fe5d0bc5b4fbcc49c0cb739b1d4bb
drwxr-xr-x root/root 0 2020-10-07 11:20 ./
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/06/
-rw-r--r-- root/root 997952 2020-10-07 11:20 ./usr/lib/debug/.build-id/06/d9ce7729891c0da8ba83050b8bf28c9e47e044.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/3b/
-rw-r--r-- root/root 929252 2020-10-07 11:20 ./usr/lib/debug/.build-id/3b/f2b7f153bb48dce5358d08b3a96005401102d6.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/47/
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drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/48/
-rw-r--r-- root/root 5403644 2020-10-07 11:20 ./usr/lib/debug/.build-id/48/4cf80b37dd6a680b0396ce83a0ba371d037651.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/5f/
-rw-r--r-- root/root 17772 2020-10-07 11:20 ./usr/lib/debug/.build-id/5f/af162a47690426da2211010d957c4dbc8d8dc9.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/69/
-rw-r--r-- root/root 124084 2020-10-07 11:20 ./usr/lib/debug/.build-id/69/213aaddf21221363be65ab9cc7435352934c97.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/9d/
-rw-r--r-- root/root 780396 2020-10-07 11:20 ./usr/lib/debug/.build-id/9d/da9757f413a090b1c3aa724aa5c1220ee3ffe8.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/a9/
-rw-r--r-- root/root 13740 2020-10-07 11:20 ./usr/lib/debug/.build-id/a9/c83e566926bfbc1b33e2fe7e9adebcfdc76b55.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/aa/
-rw-r--r-- root/root 22128 2020-10-07 11:20 ./usr/lib/debug/.build-id/aa/fa776fadeb97c818fc2dab53d69a9429ae8277.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/b7/
-rw-r--r-- root/root 902332 2020-10-07 11:20 ./usr/lib/debug/.build-id/b7/f9ea805b4b2850a709fe6d62a5ebbc6f54e5b5.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/bb/
-rw-r--r-- root/root 19352 2020-10-07 11:20 ./usr/lib/debug/.build-id/bb/4cb964cb6f226cc7141512ad592a80530abe11.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.build-id/e4/
-rw-r--r-- root/root 4719400 2020-10-07 11:20 ./usr/lib/debug/.build-id/e4/ae26f66f0fe5d0bc5b4fbcc49c0cb739b1d4bb.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 2266120 2020-10-07 11:20 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/augustus.debug
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/share/
drwxr-xr-x root/root 0 2020-10-07 11:20 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-10-07 11:20 ./usr/share/doc/augustus-dbgsym -> augustus
augustus_3.3.3+dfsg-4_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 892480 bytes: control archive=4676 bytes.
1247 bytes, 22 lines control
9874 bytes, 131 lines md5sums
Package: augustus
Version: 3.3.3+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3978
Depends: libbamtools2.5.1 (>= 2.5.1+dfsg), libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 6), zlib1g (>= 1:1.2.3.3), augustus-data
Built-Using: samtools-legacy (= 0.1.19-4)
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.
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 988456
Build-Time: 1429
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 865
Job: augustus_3.3.3+dfsg-4
Machine Architecture: armhf
Package: augustus
Package-Time: 2398
Source-Version: 3.3.3+dfsg-4
Space: 988456
Status: successful
Version: 3.3.3+dfsg-4
--------------------------------------------------------------------------------
Finished at 2020-10-09T05:35:14Z
Build needed 00:39:58, 988456k disc space