igor →
1.3.0+dfsg-1 →
armhf → 2019-02-01 06:57:44
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| igor 1.3.0+dfsg-1 (armhf) Fri, 01 Feb 2019 06:42:47 +0000 |
+==============================================================================+
Package: igor
Version: 1.3.0+dfsg-1
Source Version: 1.3.0+dfsg-1
Distribution: buster-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/buster-staging-armhf-sbuild-a4274d02-c599-4a69-8a36-89280e1c6e69' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private buster-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private buster-staging/main Sources [11.3 MB]
Get:3 http://172.17.0.1/private buster-staging/main armhf Packages [13.0 MB]
Fetched 24.3 MB in 27s (889 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: 'igor' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/igor.git
Please use:
git clone https://salsa.debian.org/med-team/igor.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 413 kB of source archives.
Get:1 http://172.17.0.1/private buster-staging/main igor 1.3.0+dfsg-1 (dsc) [1986 B]
Get:2 http://172.17.0.1/private buster-staging/main igor 1.3.0+dfsg-1 (tar) [408 kB]
Get:3 http://172.17.0.1/private buster-staging/main igor 1.3.0+dfsg-1 (diff) [3692 B]
Fetched 413 kB in 0s (4742 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/igor-egWnnd/igor-1.3.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/igor-egWnnd' 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-4wItrn/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-4wItrn/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-4wItrn/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-4wItrn/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (3041 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 16 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14049 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)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11), libjemalloc-dev, libgsl-dev, libatlas-base-dev | libcblas-dev
Filtered Build-Depends: debhelper (>= 11), libjemalloc-dev, libgsl-dev, libatlas-base-dev
dpkg-deb: building package 'sbuild-build-depends-igor-dummy' in '/<<BUILDDIR>>/resolver-4wItrn/apt_archive/sbuild-build-depends-igor-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-igor-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-4wItrn/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ Sources [521 B]
Get:5 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ Packages [591 B]
Fetched 2445 B in 1s (3364 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install igor build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
ca-certificates dbus dbus-user-session krb5-locales libexpat1
libgpg-error-l10n libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 libnss-systemd libpam-systemd libssl1.1 openssl systemd-sysv
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-7-base gettext
gettext-base groff-base intltool-debian libarchive-zip-perl
libatlas-base-dev libatlas3-base libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgsl-dev
libgsl23 libgslcblas0 libicu63 libjemalloc-dev libjemalloc2 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtool libuchardet0 libxml2 m4 man-db
po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libatlas-doc liblapack-doc gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info
| gsl-ref-html libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gcc-7-base gettext
gettext-base groff-base intltool-debian libarchive-zip-perl
libatlas-base-dev libatlas3-base libbsd0 libcroco3 libelf1
libfile-stripnondeterminism-perl libgfortran4 libglib2.0-0 libgsl-dev
libgsl23 libgslcblas0 libicu63 libjemalloc-dev libjemalloc2 libmagic-mgc
libmagic1 libpipeline1 libsigsegv2 libtool libuchardet0 libxml2 m4 man-db
po-debconf sbuild-build-depends-igor-dummy
0 upgraded, 41 newly installed, 0 to remove and 16 not upgraded.
Need to get 25.7 MB/25.9 MB of archives.
After this operation, 108 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-4wItrn/apt_archive ./ sbuild-build-depends-igor-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.0.1/private buster-staging/main armhf libbsd0 armhf 0.9.1-1 [104 kB]
Get:3 http://172.17.0.1/private buster-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:4 http://172.17.0.1/private buster-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:5 http://172.17.0.1/private buster-staging/main armhf groff-base armhf 1.22.4-2 [782 kB]
Get:6 http://172.17.0.1/private buster-staging/main armhf libpipeline1 armhf 1.5.1-1 [26.6 kB]
Get:7 http://172.17.0.1/private buster-staging/main armhf man-db armhf 2.8.5-1 [1231 kB]
Get:8 http://172.17.0.1/private buster-staging/main armhf libmagic-mgc armhf 1:5.35-2 [242 kB]
Get:9 http://172.17.0.1/private buster-staging/main armhf libmagic1 armhf 1:5.35-2 [109 kB]
Get:10 http://172.17.0.1/private buster-staging/main armhf file armhf 1:5.35-2 [65.1 kB]
Get:11 http://172.17.0.1/private buster-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:12 http://172.17.0.1/private buster-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:13 http://172.17.0.1/private buster-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:14 http://172.17.0.1/private buster-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:15 http://172.17.0.1/private buster-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:16 http://172.17.0.1/private buster-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:17 http://172.17.0.1/private buster-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:18 http://172.17.0.1/private buster-staging/main armhf libtool all 2.4.6-8 [547 kB]
Get:19 http://172.17.0.1/private buster-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:20 http://172.17.0.1/private buster-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:21 http://172.17.0.1/private buster-staging/main armhf libfile-stripnondeterminism-perl all 1.1.0-1 [19.5 kB]
Get:22 http://172.17.0.1/private buster-staging/main armhf dh-strip-nondeterminism all 1.1.0-1 [12.6 kB]
Get:23 http://172.17.0.1/private buster-staging/main armhf libelf1 armhf 0.175-2 [157 kB]
Get:24 http://172.17.0.1/private buster-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:25 http://172.17.0.1/private buster-staging/main armhf libglib2.0-0 armhf 2.58.2-3 [1076 kB]
Get:26 http://172.17.0.1/private buster-staging/main armhf libicu63 armhf 63.1-6 [7973 kB]
Get:27 http://172.17.0.1/private buster-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:28 http://172.17.0.1/private buster-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:29 http://172.17.0.1/private buster-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:30 http://172.17.0.1/private buster-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private buster-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private buster-staging/main armhf debhelper all 12 [1002 kB]
Get:33 http://172.17.0.1/private buster-staging/main armhf libgfortran4 armhf 7.3.0-19 [191 kB]
Get:34 http://172.17.0.1/private buster-staging/main armhf libatlas3-base armhf 3.10.3-7+rpi1 [2439 kB]
Get:35 http://172.17.0.1/private buster-staging/main armhf libatlas-base-dev armhf 3.10.3-7+rpi1 [3011 kB]
Get:36 http://172.17.0.1/private buster-staging/main armhf libgslcblas0 armhf 2.5+dfsg-6 [79.0 kB]
Get:37 http://172.17.0.1/private buster-staging/main armhf libgsl23 armhf 2.5+dfsg-6 [704 kB]
Get:38 http://172.17.0.1/private buster-staging/main armhf libgsl-dev armhf 2.5+dfsg-6 [893 kB]
Get:39 http://172.17.0.1/private buster-staging/main armhf libjemalloc2 armhf 5.1.0-2 [169 kB]
Get:40 http://172.17.0.1/private buster-staging/main armhf libjemalloc-dev armhf 5.1.0-2 [338 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
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Setting up libfile-stripnondeterminism-perl (1.1.0-1) ...
Setting up libgfortran4:armhf (7.3.0-19) ...
Setting up libgsl23:armhf (2.5+dfsg-6) ...
Setting up gettext (0.19.8.1-9) ...
Setting up libgsl-dev (2.5+dfsg-6) ...
Setting up groff-base (1.22.4-2) ...
Setting up autoconf (2.69-11) ...
Setting up file (1:5.35-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up man-db (2.8.5-1) ...
Not building database; man-db/auto-update is not 'true'.
Created symlink /etc/systemd/system/timers.target.wants/man-db.timer -> /lib/systemd/system/man-db.timer.
Setting up libtool (2.4.6-8) ...
Setting up libatlas3-base:armhf (3.10.3-7+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up po-debconf (1.0.21) ...
Setting up libatlas-base-dev:armhf (3.10.3-7+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
update-alternatives: using /usr/lib/arm-linux-gnueabihf/atlas/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up dh-strip-nondeterminism (1.1.0-1) ...
Setting up debhelper (12) ...
Setting up dh-autoreconf (19) ...
Setting up sbuild-build-depends-igor-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.28-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.31.1-11+rpi1 dpkg-dev_1.19.2 g++-8_8.2.0-14+rpi1 gcc-8_8.2.0-14+rpi1 libc6-dev_2.28-5+rpi1 libstdc++-8-dev_8.2.0-14+rpi1 libstdc++6_8.2.0-14+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.0~beta1 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.1+rpi1 base-passwd_3.5.45 bash_5.0-2 binutils_2.31.1-11+rpi1 binutils-arm-linux-gnueabihf_2.31.1-11+rpi1 binutils-common_2.31.1-11+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.5 bzip2_1.0.6-9 ca-certificates_20170717 coreutils_8.30-1 cpio_2.12+dfsg-6 cpp_4:8.2.0-2+rpi1 cpp-8_8.2.0-14+rpi1 dash_0.5.10.2-5 dbus_1.12.12-1 dbus-user-session_1.12.12-1 debconf_1.5.70 debhelper_12 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.0-1 diffutils_1:3.6-1 dirmngr_2.2.12-1+rpi1 dmsetup_2:1.02.155-1 dpkg_1.19.2 dpkg-dev_1.19.2 dwz_0.12-3 e2fslibs_1.44.5-1 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-2 findutils_4.6.0+git+20190105-2 g++_4:8.2.0-2+rpi1 g++-8_8.2.0-14+rpi1 gcc_4:8.2.0-2+rpi1 gcc-4.6-base_4.6.4-5+rpi1 gcc-4.7-base_4.7.3-11+rpi1 gcc-4.8-base_4.8.5-4 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1 gcc-7-base_7.3.0-19 gcc-8_8.2.0-14+rpi1 gcc-8-base_8.2.0-14+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-2 gzip_1.9-3 hostname_3.21 inetutils-ping_2:1.9.4-5 init-system-helpers_1.56+nmu1 initramfs-tools_0.132 initramfs-tools-core_0.132 intltool-debian_0.35.0+20060710.5 klibc-utils_2.0.4-15+rpi1 kmod_25-2 krb5-locales_1.17-1 libacl1_2.2.52-3 libapparmor1_2.13.2-3 libapt-pkg5.0_1.8.0~beta1 libarchive-zip-perl_1.64-1 libargon2-1_0~20171227-0.1 libasan5_8.2.0-14+rpi1 libassuan0_2.5.2-1 libatlas-base-dev_3.10.3-7+rpi1 libatlas3-base_3.10.3-7+rpi1 libatomic1_8.2.0-14+rpi1 libattr1_1:2.4.47-2 libaudit-common_1:2.8.4-2 libaudit1_1:2.8.4-2+b1 libbinutils_2.31.1-11+rpi1 libblkid1_2.33.1-0.1 libbsd0_0.9.1-1 libbz2-1.0_1.0.6-9 libc-bin_2.28-5+rpi1 libc-dev-bin_2.28-5+rpi1 libc6_2.28-5+rpi1 libc6-dev_2.28-5+rpi1 libcap-ng0_0.7.9-2 libcap2_1:2.25-1.2 libcc1-0_8.2.0-14+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libcryptsetup12_2:2.0.6-1 libcryptsetup4_2:1.7.5-1 libdb5.3_5.3.28+dfsg1-0.2 libdbus-1-3_1.12.12-1 libdebconfclient0_0.246 libdevmapper1.02.1_2:1.02.155-1 libdpkg-perl_1.19.2 libdrm-common_2.4.95-1+rpi1 libdrm2_2.4.95-1+rpi1 libelf1_0.175-2 libexpat1_2.2.6-1 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.0-1 libgcc-8-dev_8.2.0-14+rpi1 libgcc1_1:8.2.0-14+rpi1 libgcrypt20_1.8.4-4 libgdbm-compat4_1.18.1-2 libgdbm3_1.8.3-14 libgdbm6_1.18.1-2 libgfortran4_7.3.0-19 libglib2.0-0_2.58.2-3 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.5-2+rpi1 libgomp1_8.2.0-14+rpi1 libgpg-error-l10n_1.33-3 libgpg-error0_1.33-3 libgsl-dev_2.5+dfsg-6 libgsl23_2.5+dfsg-6 libgslcblas0_2.5+dfsg-6 libgssapi-krb5-2_1.17-1 libhogweed4_3.4.1~rc1-1 libicu63_63.1-6 libidn11_1.33-2.2 libidn2-0_2.0.5-1 libip4tc0_1.8.2-3 libisl19_0.20-2 libjemalloc-dev_5.1.0-2 libjemalloc2_5.1.0-2 libjson-c3_0.12.1-1.3 libk5crypto3_1.17-1 libkeyutils1_1.5.9-9.3 libklibc_2.0.4-15+rpi1 libkmod2_25-2 libkrb5-3_1.17-1 libkrb5support0_1.17-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-2 libldap-common_2.4.47+dfsg-2 liblz4-1_1.8.3-1 liblzma5_5.2.2-1.3 libmagic-mgc_1:5.35-2 libmagic1_1:5.35-2 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpfr6_4.0.2~rc1-1 libncurses5_6.1+20181013-1 libncurses6_6.1+20181013-1 libncursesw5_6.1+20181013-1 libncursesw6_6.1+20181013-1 libnettle6_3.4.1~rc1-1 libnpth0_1.6-1 libnss-systemd_240-4+rpi1 libp11-kit0_0.23.14-2 libpam-modules_1.1.8-4 libpam-modules-bin_1.1.8-4 libpam-runtime_1.1.8-4 libpam-systemd_240-4+rpi1 libpam0g_1.1.8-4 libpcre3_2:8.39-11+rpi1 libperl5.28_5.28.1-3 libpipeline1_1.5.1-1 libplymouth4_0.9.4-1 libpng16-16_1.6.36-2 libprocps7_2:3.3.15-2 libreadline7_7.0-5 libsasl2-2_2.1.27+dfsg-1 libsasl2-modules-db_2.1.27+dfsg-1 libseccomp2_2.3.3-3+b1 libselinux1_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsigsegv2_2.12-2 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.26.0+fossilbc891ac6b-1 libss2_1.44.5-1 libssl1.1_1.1.1a-1 libstdc++-8-dev_8.2.0-14+rpi1 libstdc++6_8.2.0-14+rpi1 libsystemd0_240-4+rpi1 libtasn1-6_4.13-3 libtinfo5_6.1+20181013-1 libtinfo6_6.1+20181013-1 libtool_2.4.6-8 libubsan1_8.2.0-14+rpi1 libuchardet0_0.0.6-3 libudev1_240-4+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libxml2_2.9.4+dfsg1-7+b1 libzstd1_1.3.8+dfsg-3+rpi1 linux-base_4.5 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2018112800+rpi1 m4_1.4.18-2 make_4.2.1-1.2 makedev_2.3.1-94 man-db_2.8.5-1 mawk_1.3.3-17 mount_2.33.1-0.1 multiarch-support_2.28-5+rpi1 nano_3.2-1 ncurses-base_6.1+20181013-1 ncurses-bin_6.1+20181013-1 netbase_5.5 openssl_1.1.1a-1 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-3 perl-base_5.28.1-3 perl-modules-5.28_5.28.1-3 pinentry-curses_1.1.0-1 plymouth_0.9.4-1 po-debconf_1.0.21 procps_2:3.3.15-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-igor-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 systemd_240-4+rpi1 systemd-sysv_240-4+rpi1 sysvinit-utils_2.93-5 tar_1.30+dfsg-4 tzdata_2018i-1 udev_240-4+rpi1 util-linux_2.33.1-0.1 xz-utils_5.2.2-1.3 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Jan 26 17:37:46 2019 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./igor_1.3.0+dfsg-1.dsc
dpkg-source: info: extracting igor in /<<BUILDDIR>>/igor-1.3.0+dfsg
dpkg-source: info: unpacking igor_1.3.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking igor_1.3.0+dfsg-1.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying get_autoreconf_to_work.patch
dpkg-source: info: applying inline_fix.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=buster-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=buster-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=buster-staging-armhf-sbuild-a4274d02-c599-4a69-8a36-89280e1c6e69
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package igor
dpkg-buildpackage: info: source version 1.3.0+dfsg-1
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
dh_auto_clean
rm -rf docs/latex
rm -rf docs/html
rm -rf config.guess config.sub
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
dh_clean
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:14: installing './compile'
configure.ac:14: installing './config.guess'
configure.ac:14: installing './config.sub'
configure.ac:7: installing './install-sh'
configure.ac:7: installing './missing'
igor_src/Makefile.am: installing './depcomp'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --libexecdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking how to print strings... printf
checking whether make supports the include directive... yes (GNU style)
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert arm-unknown-linux-gnueabihf file names to arm-unknown-linux-gnueabihf format... func_convert_file_noop
checking how to convert arm-unknown-linux-gnueabihf file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking for g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... none
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... yes
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) none
checking whether g++ supports C++11 features by default... yes
checking for g++ option to support OpenMP... -fopenmp
checking for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for inline... inline
checking for size_t... yes
checking for pow... yes
checking for sqrt... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating igor_src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in igor_src (/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src)
configure: WARNING: no configuration information is in igor_src
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
Making all in igor_src
make[3]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Bestscenarioscounter.o `test -f 'Bestscenarioscounter.cpp' || echo './'`Bestscenarioscounter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Counter.o `test -f 'Counter.cpp' || echo './'`Counter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Coverageerrcounter.o `test -f 'Coverageerrcounter.cpp' || echo './'`Coverageerrcounter.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp
Deletion.cpp:1590:23: warning: multi-character character constant [-Wmultichar]
else if ((*iter)=='14'){
^~~~
Deletion.cpp: In member function 'virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)':
Deletion.cpp:909:70: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
throw invalid_argument("Unknown side for D deletion: " + (*this).event_side); //TODO explicitly throw the side used
^~~~~~~~~~
Deletion.cpp:909:70: note: candidate 1: 'operator+(const char*, int)' <built-in>
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Deletion.h:29,
from Deletion.cpp:26:
Utils.h:67:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Seq_side)'
std::string operator+(const std::string& , Seq_side );
^~~~~~~~
Deletion.cpp:1173:67: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
throw invalid_argument("Unknown gene for deletions : " + this->event_class);
^~~~~~~~~~~
Deletion.cpp:1173:67: note: candidate 1: 'operator+(const char*, int)' <built-in>
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Deletion.h:29,
from Deletion.cpp:26:
Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)'
std::string operator+(const std::string& , Gene_class );
^~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Bestscenarioscounter.h:29,
from Bestscenarioscounter.cpp:26:
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_emplace_aux(std::vector<_Tp, _Alloc>::const_iterator, _Args&& ...) [with _Args = {long double&, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >&, std::__cxx11::list<int, std::allocator<int> >&}; _Tp = std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >; _Alloc = std::allocator<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >]':
/usr/include/c++/8/bits/vector.tcc:351:7: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::const_iterator' {aka '__gnu_cxx::__normal_iterator<const std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >*, std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:351:7: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::const_iterator' {aka '__gnu_cxx::__normal_iterator<const std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >*, std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > > >'} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Bestscenarioscounter.h:29,
from Bestscenarioscounter.cpp:26:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Best_scenarios_counter::count_scenario(long double, double, const string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Mismatch_vectors_map&)':
/usr/include/c++/8/bits/stl_vector.h:1136:68: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::const_iterator' {aka '__gnu_cxx::__normal_iterator<const std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >*, std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > > >'} changed in GCC 7.1
{ return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
^
/usr/include/c++/8/bits/stl_vector.h:1136:68: note: parameter passing for argument of type 'std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > >::const_iterator' {aka '__gnu_cxx::__normal_iterator<const std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > >*, std::vector<std::tuple<double, std::queue<std::vector<int, std::allocator<int> >, std::deque<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > > >, std::__cxx11::list<int, std::allocator<int> > > > >'} changed in GCC 7.1
{ return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
^
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp
Deletion.cpp: In member function 'virtual bool Deletion::has_effect_on(Seq_type) const':
Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type]
}
^
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp
Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)':
Dinuclmarkov.cpp:147:81: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
^~~~~~~~~~~
Dinuclmarkov.cpp:147:81: note: candidate 1: 'operator+(const char*, int)' <built-in>
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Dinuclmarkov.h:32,
from Dinuclmarkov.cpp:26:
Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)'
std::string operator+(const std::string& , Gene_class );
^~~~~~~~
Dinuclmarkov.cpp: In member function 'virtual std::queue<int> Dinucl_markov::draw_random_realization(const Marginal_array_p&, std::unordered_map<std::__cxx11::basic_string<char>, int>&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::unordered_map<Seq_type, std::__cxx11::basic_string<char> >&, std::mt19937_64&) const':
Dinuclmarkov.cpp:211:81: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
^~~~~~~~~~~
Dinuclmarkov.cpp:211:81: note: candidate 1: 'operator+(const char*, int)' <built-in>
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Dinuclmarkov.h:32,
from Dinuclmarkov.cpp:26:
Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)'
std::string operator+(const std::string& , Gene_class );
^~~~~~~~
Dinuclmarkov.cpp: In member function 'virtual void Dinucl_markov::iterate_initialize_Len_proba(Seq_type, std::map<int, double>&, std::queue<std::shared_ptr<Rec_Event> >&, double&, const Marginal_array_p&, Index_map&, Seq_type_str_p_map&, int&) const':
Dinuclmarkov.cpp:566:81: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
^~~~~~~~~~~
Dinuclmarkov.cpp:566:81: note: candidate 1: 'operator+(const char*, int)' <built-in>
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Dinuclmarkov.h:32,
from Dinuclmarkov.cpp:26:
Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)'
std::string operator+(const std::string& , Gene_class );
^~~~~~~~
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Dinuclmarkov.h:32,
from Dinuclmarkov.cpp:26:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:140:2: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from /usr/include/c++/8/vector:69,
from Utils.h:31,
from Aligner.h:37,
from Aligner.cpp:27:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function 'Matrix<double> read_substitution_matrix(const string&, std::__cxx11::string)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Alignment_data}; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<Alignment_data>::iterator' {aka '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/c++/8/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Errorscounter.h:29,
from Errorscounter.cpp:26:
/usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_emplace_aux(std::vector<_Tp, _Alloc>::const_iterator, _Args&& ...) [with _Args = {long double&, unsigned int&, unsigned int&}; _Tp = std::tuple<double, unsigned int, unsigned int>; _Alloc = std::allocator<std::tuple<double, unsigned int, unsigned int> >]':
/usr/include/c++/8/bits/vector.tcc:351:7: note: parameter passing for argument of type 'std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator' {aka '__gnu_cxx::__normal_iterator<const std::tuple<double, unsigned int, unsigned int>*, std::vector<std::tuple<double, unsigned int, unsigned int> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/c++/8/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Errorscounter.h:29,
from Errorscounter.cpp:26:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Errors_counter::count_scenario(long double, double, const string&, Seq_type_str_p_map&, const Seq_offsets_map&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Mismatch_vectors_map&)':
/usr/include/c++/8/bits/stl_vector.h:1136:68: note: parameter passing for argument of type 'std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator' {aka '__gnu_cxx::__normal_iterator<const std::tuple<double, unsigned int, unsigned int>*, std::vector<std::tuple<double, unsigned int, unsigned int> > >'} changed in GCC 7.1
{ return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
^
/usr/include/c++/8/bits/stl_vector.h:1136:68: note: parameter passing for argument of type 'std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator' {aka '__gnu_cxx::__normal_iterator<const std::tuple<double, unsigned int, unsigned int>*, std::vector<std::tuple<double, unsigned int, unsigned int> > >'} changed in GCC 7.1
{ return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
^
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorrate.o `test -f 'Errorrate.cpp' || echo './'`Errorrate.cpp
In file included from /usr/include/c++/8/bits/stl_algobase.h:71,
from /usr/include/c++/8/bits/forward_list.h:38,
from /usr/include/c++/8/forward_list:38,
from Aligner.h:29,
from Aligner.cpp:27:
/usr/include/c++/8/bits/predefined_ops.h: In member function 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Iterator2 = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Compare = bool (*)(Alignment_data, Alignment_data)]':
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Aligner.cpp:27:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp
In file included from /usr/include/c++/8/vector:69,
from Utils.h:31,
from Aligner.h:37,
from Aligner.cpp:27:
/usr/include/c++/8/bits/vector.tcc: In function 'std::unordered_map<int, std::vector<Alignment_data> > read_alignments_seq_csv(std::__cxx11::string, double, bool)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Aligner.cpp:27:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Distance = int; _Tp = Alignment_data; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
__pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_heap.h:243:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Aligner.cpp:27:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:81:17: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
if (__comp(__a, __b))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'std::unordered_map<int, std::pair<std::__cxx11::basic_string<char>, std::unordered_map<Gene_class, std::vector<Alignment_data> > > > read_alignments_seq_csv_score_range(std::__cxx11::string, Gene_class, double, bool, std::vector<std::pair<const int, const std::__cxx11::basic_string<char> > >, std::unordered_map<int, std::pair<std::__cxx11::basic_string<char>, std::unordered_map<Gene_class, std::vector<Alignment_data> > > >)':
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp
Genechoice.cpp: In member function 'virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)':
Genechoice.cpp:908:73: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
throw invalid_argument("Unknown gene_class for GeneChoice: " + this->event_class);
^~~~~~~~~~~
Genechoice.cpp:908:73: note: candidate 1: 'operator+(const char*, int)' <built-in>
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Genechoice.h:29,
from Genechoice.cpp:26:
Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)'
std::string operator+(const std::string& , Gene_class );
^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp
In file included from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:140:2: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from /usr/include/c++/8/vector:69,
from Utils.h:31,
from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from Errorrate.h:29,
from Hypermutationglobalerrorrate.h:30,
from Hypermutationglobalerrorrate.cpp:27:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:140:2: warning: control reaches end of non-void function [-Wreturn-type]
}
^
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from HypermutationfullNmererrorrate.h:31,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from Rec_Event.h:32,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, const int&, const int&, double}; _Tp = std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>; _Alloc = std::allocator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> >]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> >::iterator' {aka '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algobase.h:71,
from /usr/include/c++/8/bits/char_traits.h:39,
from /usr/include/c++/8/string:40,
from /usr/include/c++/8/stdexcept:39,
from /usr/include/c++/8/array:39,
from /usr/include/c++/8/tuple:39,
from /usr/include/c++/8/bits/hashtable_policy.h:34,
from /usr/include/c++/8/bits/hashtable.h:35,
from /usr/include/c++/8/unordered_map:46,
from Rec_Event.h:30,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/8/bits/predefined_ops.h: In member function 'constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Iterator2 = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Compare = D_position_comparator]':
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
operator()(_Iterator1 __it1, _Iterator2 __it2)
^~~~~~~~
/usr/include/c++/8/bits/predefined_ops.h:142:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<D_position_comparator>]':
/usr/include/c++/8/bits/stl_algo.h:1821:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
__unguarded_linear_insert(_RandomAccessIterator __last,
^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/queue:62,
from Errorrate.h:38,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/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++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from HypermutationfullNmererrorrate.h:31,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/queue:62,
from Rec_Event.h:37,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__push_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Distance = int; _Tp = std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_val<D_position_comparator>]':
/usr/include/c++/8/bits/stl_heap.h:128:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
__push_heap(_RandomAccessIterator __first,
^~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from Utils.h:31,
from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Hypermutation_full_Nmer_errorrate::build_upper_bound_matrix(size_t, size_t)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from HypermutationfullNmererrorrate.h:31,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Distance = int; _Tp = std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/8/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]':
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:83:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:85:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:90:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
else if (__comp(__a, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:92:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
else if (__comp(__b, __c))
~~~~~~^~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from Rec_Event.h:32,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/8/bits/vector.tcc: In member function 'virtual void Gene_choice::initialize_Len_proba_bound(std::queue<std::shared_ptr<Rec_Event> >&, const Marginal_array_p&, Index_map&)':
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from Utils.h:31,
from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual void Hypermutation_full_Nmer_errorrate::update()':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from HypermutationfullNmererrorrate.h:31,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from Rec_Event.h:32,
from Model_Parms.h:33,
from GenModel.h:32,
from GenModel.cpp:28:
/usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Alignment_data&}; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]':
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<Alignment_data>::iterator' {aka '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from Utils.h:31,
from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/bits/stl_vector.h: In member function 'virtual const double& Hypermutation_full_Nmer_errorrate::get_err_rate_upper_bound(size_t, size_t)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from HypermutationfullNmererrorrate.h:31,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from Rec_Event.h:32,
from Model_Parms.h:33,
from GenModel.h:32,
from GenModel.cpp:28:
/usr/include/c++/8/bits/stl_vector.h: In function 'std::vector<std::tuple<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::unordered_map<Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> >, std::hash<Gene_class>, std::equal_to<Gene_class>, std::allocator<std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > > > > > > get_best_aligns(const std::vector<std::tuple<int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::unordered_map<Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> >, std::hash<Gene_class>, std::equal_to<Gene_class>, std::allocator<std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > > > > > >&, Gene_class)':
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-IntStr.o `test -f 'IntStr.cpp' || echo './'`IntStr.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp
Insertion.cpp: In member function 'virtual void Insertion::iterate(double&, Downstream_scenario_proba_bound_map&, const string&, const Int_Str&, Index_map&, const std::unordered_map<std::__cxx11::basic_string<char>, std::vector<std::pair<std::shared_ptr<const Rec_Event>, int> > >&, std::shared_ptr<Rec_Event*>&, Marginal_array_p&, const Marginal_array_p&, const std::unordered_map<Gene_class, std::vector<Alignment_data> >&, Seq_type_str_p_map&, Seq_offsets_map&, std::shared_ptr<Error_rate>&, std::map<unsigned int, std::shared_ptr<Counter> >&, const std::unordered_map<std::tuple<Event_type, Gene_class, Seq_side>, std::shared_ptr<Rec_Event> >&, Safety_bool_map&, Mismatch_vectors_map&, double&, double&)':
Insertion.cpp:244:72: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
throw invalid_argument("Unknown gene_class for Insertion: " + this->event_class);
^~~~~~~~~~~
Insertion.cpp:244:72: note: candidate 1: 'operator+(const char*, int)' <built-in>
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Insertion.h:30,
from Insertion.cpp:27:
Utils.h:66:13: note: candidate 2: 'std::__cxx11::string operator+(const string&, Gene_class)'
std::string operator+(const std::string& , Gene_class );
^~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.cpp
main.cpp: In function 'int main(int, char**)':
main.cpp:241:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(&("man igor")[0]);
~~~~~~^~~~~~~~~~~~~~~~~~
main.cpp:265:11: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
freopen(argv[++carg_i],"a+",stdout);
~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1480:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(&("mkdir " + cl_path )[0]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1631:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(&("mkdir " + cl_path + "run_demo")[0]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1665:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(&("mkdir " + cl_path + "aligns")[0]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1929:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(&("mkdir " + cl_path + batchname + "output")[0]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1933:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(&("mkdir " + cl_path + batchname + "inference")[0]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1939:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(&("mkdir " + cl_path + batchname + "evaluate")[0]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1949:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
system(&("mkdir " + cl_path + batchname + "generated")[0]);
~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from Errorrate.h:29,
from Rec_Event.h:38,
from Deletion.h:29,
from main.cpp:28:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:140:2: warning: control reaches end of non-void function [-Wreturn-type]
}
^
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.cpp
In file included from /usr/include/c++/8/vector:69,
from Rec_Event.h:32,
from Model_Parms.h:33,
from Model_Parms.cpp:30:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/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++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp
In file included from Errorrate.h:29,
from Singleerrorrate.h:30,
from Singleerrorrate.cpp:27:
Utils.h: In member function 'Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]':
Utils.h:140:2: warning: control reaches end of non-void function [-Wreturn-type]
}
^
/bin/bash ../libtool --tag=CXX --mode=link g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-main.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o -lgsl -lcblas -ljemalloc -lpthread -ldl
libtool: link: g++ -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/igor-1.3.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -Wl,--as-needed -o igor igor-Aligner.o igor-Bestscenarioscounter.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-main.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o -lgsl -lcblas -ljemalloc -lpthread -ldl -fopenmp
make[3]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src'
make[3]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
Making check in igor_src
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src'
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_installdirs -a
dh_auto_install -a
make -j1 install DESTDIR=/<<BUILDDIR>>/igor-1.3.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
Making install in igor_src
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src'
make[3]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src'
/bin/mkdir -p '/<<BUILDDIR>>/igor-1.3.0+dfsg/debian/igor/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c igor '/<<BUILDDIR>>/igor-1.3.0+dfsg/debian/igor/usr/bin'
libtool: install: /usr/bin/install -c igor /<<BUILDDIR>>/igor-1.3.0+dfsg/debian/igor/usr/bin/igor
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src'
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg/igor_src'
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[3]: Nothing to be done for 'install-exec-am'.
mkdir -p /<<BUILDDIR>>/igor-1.3.0+dfsg/debian/igor/usr/share/igor/models
cp -r models/* /<<BUILDDIR>>/igor-1.3.0+dfsg/debian/igor/usr/share/igor/models
/bin/mkdir -p '/<<BUILDDIR>>/igor-1.3.0+dfsg/debian/igor/usr/share/igor/demo'
/usr/bin/install -c -m 644 demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJs_all_curated.fasta demo/murugan_naive1_noncoding_demo_seqs.txt '/<<BUILDDIR>>/igor-1.3.0+dfsg/debian/igor/usr/share/igor/demo'
make[3]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.3.0+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/igor/usr/bin/igor contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/igor/usr/bin/igor was not linked against ld-linux-armhf.so.3 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/igor/usr/bin/igor was not linked against libcblas.so.3 (it uses none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'igor-dbgsym' in '../igor-dbgsym_1.3.0+dfsg-1_armhf.deb'.
dpkg-deb: building package 'igor' in '../igor_1.3.0+dfsg-1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../igor_1.3.0+dfsg-1_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 2019-02-01T06:57:37Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
igor_1.3.0+dfsg-1_armhf.changes:
--------------------------------
Format: 1.8
Date: Sat, 26 Jan 2019 17:21:02 +0100
Source: igor
Binary: igor
Architecture: armhf
Version: 1.3.0+dfsg-1
Distribution: buster-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
igor - infers V(D)J recombination processes from sequencing data
Changes:
igor (1.3.0+dfsg-1) unstable; urgency=medium
.
* Team upload.
* Debian Med team maintenance
* Fix watch file
* Standards-Version: 4.2.1
* Add missing Build-Depends: libatlas-base-dev | libcblas-dev
* Fix for gcc-8 does not expose inline definitions to other source files
* hardening=+all
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32e3caadccc549579da7ded9276fa305567cf3d7 4743 igor_1.3.0+dfsg-1_armhf.buildinfo
35ceda6c4143cb0439d46c02945007326037217f 450760 igor_1.3.0+dfsg-1_armhf.deb
Checksums-Sha256:
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faa98e992cd3e196a5470349cff768a8ca9e3c3c59b2b65d238fbdb6603fbce2 4743 igor_1.3.0+dfsg-1_armhf.buildinfo
3f372e3925902da813f42782fa57e54d31f498e7ff52f215b17b8b00501b7f19 450760 igor_1.3.0+dfsg-1_armhf.deb
Files:
ab5985ac02aece0d0e9c8e863f1fa5fc 5993304 debug optional igor-dbgsym_1.3.0+dfsg-1_armhf.deb
55386be96a19c743596e2a8881a47661 4743 science optional igor_1.3.0+dfsg-1_armhf.buildinfo
d8c5a58f1e8f599e70a987ab8356e3bd 450760 science optional igor_1.3.0+dfsg-1_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
igor-dbgsym_1.3.0+dfsg-1_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 5993304 bytes: control archive=536 bytes.
369 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: igor-dbgsym
Source: igor
Version: 1.3.0+dfsg-1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6112
Depends: igor (= 1.3.0+dfsg-1)
Section: debug
Priority: optional
Description: debug symbols for igor
Build-Ids: dfe4978c387f09ce836f536888fd3df933436584
drwxr-xr-x root/root 0 2019-01-26 16:21 ./
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/lib/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/lib/debug/.build-id/df/
-rw-r--r-- root/root 6248384 2019-01-26 16:21 ./usr/lib/debug/.build-id/df/e4978c387f09ce836f536888fd3df933436584.debug
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-01-26 16:21 ./usr/share/doc/igor-dbgsym -> igor
igor_1.3.0+dfsg-1_armhf.deb
---------------------------
new Debian package, version 2.0.
size 450760 bytes: control archive=2140 bytes.
625 bytes, 13 lines control
5955 bytes, 59 lines md5sums
Package: igor
Version: 1.3.0+dfsg-1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2250
Depends: libatlas3-base, libc6 (>= 2.4), libgcc1 (>= 1:3.5), libgomp1 (>= 4.9), libgsl23 (>= 2.5), libjemalloc2 (>= 5.0.0), libstdc++6 (>= 5.2)
Section: science
Priority: optional
Homepage: https://github.com/qmarcou/IGoR/
Description: infers V(D)J recombination processes from sequencing data
IGoR (Inference and Generation of Repertoires) is a versatile software
to analyze and model immune receptors generation, selection, mutation
and all other processes.
drwxr-xr-x root/root 0 2019-01-26 16:21 ./
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/bin/
-rwxr-xr-x root/root 677384 2019-01-26 16:21 ./usr/bin/igor
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/doc/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/doc/igor/
-rw-r--r-- root/root 398 2019-01-26 16:21 ./usr/share/doc/igor/changelog.Debian.gz
-rw-r--r-- root/root 1056 2018-08-04 19:27 ./usr/share/doc/igor/changelog.gz
-rw-r--r-- root/root 1090 2019-01-26 16:21 ./usr/share/doc/igor/copyright
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/demo/
-rw-r--r-- root/root 84 2019-01-26 16:21 ./usr/share/igor/demo/genomicDs.fasta
-rw-r--r-- root/root 2022 2019-01-26 16:21 ./usr/share/igor/demo/genomicJs_all_curated.fasta
-rw-r--r-- root/root 33856 2019-01-26 16:21 ./usr/share/igor/demo/genomicVs_with_primers.fasta
-rw-r--r-- root/root 18300 2019-01-26 16:21 ./usr/share/igor/demo/murugan_naive1_noncoding_demo_seqs.txt
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/
-rw-r--r-- root/root 690 2019-01-26 16:21 ./usr/share/igor/models/heavy_pen_substitution_matrix.csv
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/
-rw-r--r-- root/root 523 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/model.info
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/models/
-rw-r--r-- root/root 483313 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/models/model_marginals.txt
-rw-r--r-- root/root 35291 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/models/model_parms.txt
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/ref_genome/
-rw-r--r-- root/root 102 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/ref_genome/J_gene_CDR3_anchors.csv
-rw-r--r-- root/root 1151 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/ref_genome/V_gene_CDR3_anchors.csv
-rw-r--r-- root/root 1335 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/ref_genome/genomicDs.fasta
-rw-r--r-- root/root 464 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 30236 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/
-rw-r--r-- root/root 35439 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_3mer_D_hyperm_parms.txt
-rw-r--r-- root/root 35438 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_3mer_J_hyperm_parms.txt
-rw-r--r-- root/root 35441 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_3mer_V_hyperm_parms.txt
-rw-r--r-- root/root 35516 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_5mer_D_hyperm_parms.txt
-rw-r--r-- root/root 35514 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_5mer_J_hyperm_parms.txt
-rw-r--r-- root/root 35517 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_5mer_V_hyperm_parms.txt
-rw-r--r-- root/root 35599 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_7mer_D_hyperm_parms.txt
-rw-r--r-- root/root 35597 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_7mer_J_hyperm_parms.txt
-rw-r--r-- root/root 35599 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_7mer_V_hyperm_parms.txt
-rw-r--r-- root/root 35684 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_9mer_D_hyperm_parms.txt
-rw-r--r-- root/root 35672 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_9mer_J_hyperm_parms.txt
-rw-r--r-- root/root 35679 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_9mer_V_hyperm_parms.txt
-rw-r--r-- root/root 48 2019-01-26 16:21 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/models.info
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/
-rw-r--r-- root/root 489 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/model.info
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/models/
-rw-r--r-- root/root 75679 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/models/model_marginals.txt
-rw-r--r-- root/root 35883 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/models/model_parms.txt
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/ref_genome/
-rw-r--r-- root/root 18 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/ref_genome/J_gene_CDR3_anchors.csv
-rw-r--r-- root/root 18 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/ref_genome/V_gene_CDR3_anchors.csv
-rw-r--r-- root/root 4983 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 29702 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_alpha/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/
-rw-r--r-- root/root 488 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/model.info
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/models/
-rw-r--r-- root/root 114449 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/models/model_marginals.txt
-rw-r--r-- root/root 38434 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/models/model_parms.txt
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/ref_genome/
-rw-r--r-- root/root 1292 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/ref_genome/J_gene_CDR3_anchors.csv
-rw-r--r-- root/root 8254 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/ref_genome/V_gene_CDR3_anchors.csv
-rw-r--r-- root/root 84 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/ref_genome/genomicDs.fasta
-rw-r--r-- root/root 2022 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 33856 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_1/
-rw-r--r-- root/root 32903 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_1/final_marginals.txt
-rw-r--r-- root/root 38249 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_1/final_parms.txt
-rw-r--r-- root/root 35 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_1/model.info
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_4/
-rw-r--r-- root/root 33314 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_4/final_marginals.txt
-rw-r--r-- root/root 38249 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_4/final_parms.txt
-rw-r--r-- root/root 35 2019-01-26 16:21 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_4/model.info
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/mouse/
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/
-rw-r--r-- root/root 436 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/model.info
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/models/
-rw-r--r-- root/root 12795 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/models/model_marginals.txt
-rw-r--r-- root/root 13475 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/models/model_parms.txt
drwxr-xr-x root/root 0 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/
-rw-r--r-- root/root 257 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/J_gene_CDR3_anchors.csv
-rw-r--r-- root/root 448 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/V_gene_CDR3_anchors.csv
-rw-r--r-- root/root 48 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/genomicDs.fasta
-rw-r--r-- root/root 871 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 10417 2019-01-26 16:21 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/genomicVs.fasta
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 80404
Build-Time: 475
Distribution: buster-staging
Host Architecture: armhf
Install-Time: 365
Job: igor_1.3.0+dfsg-1
Machine Architecture: armhf
Package: igor
Package-Time: 890
Source-Version: 1.3.0+dfsg-1
Space: 80404
Status: successful
Version: 1.3.0+dfsg-1
--------------------------------------------------------------------------------
Finished at 2019-02-01T06:57:37Z
Build needed 00:14:50, 80404k disc space