igor →
1.4.0+dfsg-2 →
armhf → 2020-08-08 11:55:04
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| igor 1.4.0+dfsg-2 (armhf) Sat, 08 Aug 2020 11:41:52 +0000 |
+==============================================================================+
Package: igor
Version: 1.4.0+dfsg-2
Source Version: 1.4.0+dfsg-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-97bc6fbb-4ab4-41d9-be31-708356cafc01' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.8 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.7 MB in 26s (950 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 1009 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main igor 1.4.0+dfsg-2 (dsc) [2046 B]
Get:2 http://172.17.0.1/private bullseye-staging/main igor 1.4.0+dfsg-2 (tar) [1001 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main igor 1.4.0+dfsg-2 (diff) [4988 B]
Fetched 1009 kB in 0s (6357 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/igor-AXNGOG/igor-1.4.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/igor-AXNGOG' 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-g8cscp/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-g8cscp/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-g8cscp/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-g8cscp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2751 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 22 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-g8cscp/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 ... 12536 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-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev | libblas.so
Filtered Build-Depends: debhelper-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev
dpkg-deb: building package 'sbuild-build-depends-igor-dummy' in '/<<BUILDDIR>>/resolver-g8cscp/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-g8cscp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ Sources [517 B]
Get:5 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ Packages [591 B]
Fetched 2441 B in 1s (3260 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libblas-dev libblas3 libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libgsl-dev libgsl25 libgslcblas0 libicu67 libjemalloc-dev libjemalloc2
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff 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 debhelper dh-autoreconf
dh-strip-nondeterminism dwz file gettext gettext-base groff-base
intltool-debian libarchive-zip-perl libblas-dev libblas3 libcroco3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libglib2.0-0
libgsl-dev libgsl25 libgslcblas0 libicu67 libjemalloc-dev libjemalloc2
libmagic-mgc libmagic1 libpipeline1 libsigsegv2 libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-igor-dummy
0 upgraded, 39 newly installed, 0 to remove and 22 not upgraded.
Need to get 21.0 MB of archives.
After this operation, 79.6 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-g8cscp/apt_archive ./ sbuild-build-depends-igor-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-3 [801 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2 [187 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.180-1 [162 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.4-1 [1159 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-3 [8287 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5+b1 [593 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2 [1007 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-2 [108 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-2 [113 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libgslcblas0 armhf 2.6+dfsg-2 [79.5 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libgsl25 armhf 2.6+dfsg-2 [753 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libgsl-dev armhf 2.6+dfsg-2 [950 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libjemalloc2 armhf 5.2.1-1 [182 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libjemalloc-dev armhf 5.2.1-1 [409 kB]
debconf: delaying package configuration, since apt-utils is not installed
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update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libsigsegv2:armhf (2.12-2) ...
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2) ...
Setting up sbuild-build-depends-igor-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-2+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34.90.20200706-1+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-15+rpi1 gcc-9_9.3.0-15+rpi1 libc6-dev_2.31-2+rpi1 libstdc++-9-dev_9.3.0-15+rpi1 libstdc++6_10.1.0-6+rpi1 linux-libc-dev_5.7.6-1+rpi1
Package versions: adduser_3.118 apt_2.1.7 aptitude_0.8.13-1+b1 aptitude-common_0.8.13-1 autoconf_2.69-11.1 automake_1:1.16.2-3 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34.90.20200706-1+rpi1 binutils-arm-linux-gnueabihf_2.34.90.20200706-1+rpi1 binutils-common_2.34.90.20200706-1+rpi1 bsdextrautils_2.36-1 bsdutils_1:2.36-1 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-15+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.36-1 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-15+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-6+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-6+rpi1 gcc-8-base_8.4.0-4+rpi1 gcc-9_9.3.0-15+rpi1 gcc-9-base_9.3.0-15+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-8 libapt-pkg6.0_2.1.7 libarchive-zip-perl_1.68-1 libasan5_9.3.0-15+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.1.0-6+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34.90.20200706-1+rpi1 libblas-dev_3.9.0-2 libblas3_3.9.0-2 libblkid1_2.36-1 libboost-iostreams1.71.0_1.71.0-6+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-2+rpi1 libc-dev-bin_2.31-2+rpi1 libc6_2.31-2+rpi1 libc6-dev_2.31-2+rpi1 libcap-ng0_0.7.9-2.2 libcc1-0_10.1.0-6+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34.90.20200706-1+rpi1 libctf0_2.34.90.20200706-1+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.253 libdebhelper-perl_13.2 libdpkg-perl_1.19.7 libelf1_0.180-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.36-1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libgcc-9-dev_9.3.0-15+rpi1 libgcc-s1_10.1.0-6+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.4-1 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.14-2+b1 libgomp1_10.1.0-6+rpi1 libgpg-error0_1.38-2 libgsl-dev_2.6+dfsg-2 libgsl25_2.6+dfsg-2 libgslcblas0_2.6+dfsg-2 libhogweed6_3.6-2 libicu67_67.1-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libjemalloc-dev_5.2.1-1 libjemalloc2_5.2.1-1 libksba8_1.4.0-2 libldap-2.4-2_2.4.50+dfsg-1+b1 libldap-common_2.4.50+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-1 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle8_3.6-2 libnpth0_1.6-2 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.30_5.30.3-4 libpipeline1_1.5.2-2 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.2-1 libsigsegv2_2.12-2 libsmartcols1_2.36-1 libsqlite3-0_3.32.3-1 libss2_1.45.6-1 libstdc++-9-dev_9.3.0-15+rpi1 libstdc++6_10.1.0-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.6-2+rpi1+b1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-6+rpi1 libuchardet0_0.0.7-1 libudev1_245.6-2+rpi1+b1 libunistring2_0.9.10-4 libuuid1_2.36-1 libxapian30_1.4.15-1 libxml2_2.9.10+dfsg-5+b1 libzstd1_1.4.5+dfsg-3+rpi1 linux-libc-dev_5.7.6-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.3-2 mawk_1.3.4.20200120-2 mount_2.36-1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.3-4 perl-base_5.30.3-4 perl-modules-5.30_5.30.3-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 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+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.36-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Aug 5 16:53:54 2020 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_1.4.0+dfsg-2.dsc
dpkg-source: info: extracting igor in /<<BUILDDIR>>/igor-1.4.0+dfsg
dpkg-source: info: unpacking igor_1.4.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking igor_1.4.0+dfsg-2.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
dpkg-source: info: applying fix-gcc-10.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=root
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-97bc6fbb-4ab4-41d9-be31-708356cafc01
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package igor
dpkg-buildpackage: info: source version 1.4.0+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
dh_auto_clean
rm -rf docs/latex
rm -rf docs/html
rm -rf config.guess config.sub
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
dh_clean
debian/rules binary-arch
dh binary-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-option-checking --disable-silent-rules --libdir=\${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... no
checking if : 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-1.4.0+dfsg/igor_src)
configure: WARNING: no configuration information is in igor_src
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
Making all in igor_src
make[3]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+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-1.4.0+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-1.4.0+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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-CDR3SeqData.o `test -f 'CDR3SeqData.cpp' || echo './'`CDR3SeqData.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-1.4.0+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-1.4.0+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-1.4.0+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]
1590 | 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:
909 | 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:69:13: note: candidate 2: 'std::string operator+(const string&, Seq_side)'
69 | 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:
1173 | 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:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)'
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Bestscenarioscounter.h:29,
from Bestscenarioscounter.cpp:26:
/usr/include/c++/9/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++/9/bits/vector.tcc:364:7: 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
364 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:364:7: 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++/9/vector:67,
from /usr/include/c++/9/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Bestscenarioscounter.h:29,
from Bestscenarioscounter.cpp:26:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1246:68: 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
1246 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1246:68: 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
1246 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ^
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]
1705 | }
| ^
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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.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-1.4.0+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:
147 | 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:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)'
68 | 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:
211 | 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:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)'
68 | 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:565:81: 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:
565 | throw invalid_argument("Unknown gene class for DincuclMarkov model: " + this->event_class);
| ^~~~~~~~~~~
Dinuclmarkov.cpp:565:81: 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:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)'
68 | 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:142:2: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Errorscounter.h:29,
from Errorscounter.cpp:26:
/usr/include/c++/9/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++/9/bits/vector.tcc:364:7: 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
364 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Errorscounter.h:29,
from Errorscounter.cpp:26:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1246:68: 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
1246 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ^
/usr/include/c++/9/bits/stl_vector.h:1246:68: 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
1246 | { 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-1.4.0+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++/9/vector:72,
from Utils.h:31,
from Aligner.h:37,
from Aligner.cpp:27:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:426:7: 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
/usr/include/c++/9/bits/vector.tcc: In function 'Matrix<double> read_substitution_matrix(const string&, std::string)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp
In file included from /usr/include/c++/9/algorithm:62,
from Aligner.h:35,
from Aligner.cpp:27:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
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:
908 | 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:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)'
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/vector:72,
from Utils.h:31,
from Aligner.h:37,
from Aligner.cpp:27:
/usr/include/c++/9/bits/vector.tcc: In function 'std::unordered_map<int, std::vector<Alignment_data> > read_alignments_seq_csv(std::string, double, bool)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from Aligner.h:35,
from Aligner.cpp:27:
/usr/include/c++/9/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++/9/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
214 | __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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.cpp
In file included from /usr/include/c++/9/algorithm:62,
from Aligner.h:35,
from Aligner.cpp:27:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:142:2: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
/usr/include/c++/9/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::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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from Utils.h:31,
from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from Rec_Event.h:32,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1820:5: 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
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/stl_algo.h:1839:5: 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
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: 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++/9/queue:62,
from Rec_Event.h:37,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/9/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++/9/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
128 | __push_heap(_RandomAccessIterator __first,
| ^~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__final_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++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1879 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1879:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/9/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++/9/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
326 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/9/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++/9/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/9/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++/9/bits/stl_algo.h:1939:5: 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
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: 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++/9/bits/stl_algo.h:1953:25: 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
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1671:23: 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
1671 | std::__make_heap(__first, __middle, __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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Hypermutationglobalerrorrate.o `test -f 'Hypermutationglobalerrorrate.cpp' || echo './'`Hypermutationglobalerrorrate.cpp
In file included from /usr/include/c++/9/vector:72,
from Rec_Event.h:32,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: 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
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from Genechoice.cpp:26:
/usr/include/c++/9/bits/stl_algo.h:1967:25: 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
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: 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
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: 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
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from Rec_Event.h:32,
from Model_Parms.h:33,
from GenModel.h:32,
from GenModel.cpp:28:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/queue:62,
from Errorrate.h:38,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/9/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++/9/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
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/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++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from Utils.h:31,
from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void Hypermutation_full_Nmer_errorrate::build_upper_bound_matrix(size_t, size_t)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from Utils.h:31,
from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void Hypermutation_full_Nmer_errorrate::update()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from Utils.h:31,
from Errorrate.h:29,
from HypermutationfullNmererrorrate.h:30,
from HypermutationfullNmererrorrate.cpp:27:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/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++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1970:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1970 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from Rec_Event.h:32,
from Model_Parms.h:33,
from GenModel.h:32,
from GenModel.cpp:28:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
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:142:2: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
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-1.4.0+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-1.4.0+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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_marginals.o `test -f 'Model_marginals.cpp' || echo './'`Model_marginals.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:
244 | 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:68:13: note: candidate 2: 'std::string operator+(const string&, Gene_class)'
68 | 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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Model_Parms.o `test -f 'Model_Parms.cpp' || echo './'`Model_Parms.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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Pgencounter.o `test -f 'Pgencounter.cpp' || echo './'`Pgencounter.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-1.4.0+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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp
In file included from /usr/include/c++/9/vector:72,
from Rec_Event.h:32,
from Model_Parms.h:33,
from Model_Parms.cpp:30:
/usr/include/c++/9/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++/9/bits/vector.tcc:426:7: 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
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from 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:142:2: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.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-1.4.0+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-main.o `test -f 'main.cpp' || echo './'`main.cpp
main.cpp: In function 'int main(int, char**)':
main.cpp:257:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
257 | system(&("man igor")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~
main.cpp:289:11: warning: ignoring return value of 'FILE* freopen(const char*, const char*, FILE*)', declared with attribute warn_unused_result [-Wunused-result]
289 | freopen(argv[++carg_i],"a+",stdout);
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1565:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
1565 | system(&("mkdir " + cl_path )[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1716:9: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
1716 | system(&("mkdir " + cl_path + "run_demo")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:1750:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
1750 | system(&("mkdir " + cl_path + "aligns")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:2058:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
2058 | system(&("mkdir " + cl_path + batchname + "output")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:2062:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
2062 | system(&("mkdir " + cl_path + batchname + "inference")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:2068:11: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
2068 | system(&("mkdir " + cl_path + batchname + "evaluate")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
main.cpp:2078:10: warning: ignoring return value of 'int system(const char*)', declared with attribute warn_unused_result [-Wunused-result]
2078 | 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:142:2: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
/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-1.4.0+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-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -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-1.4.0+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-CDR3SeqData.o igor-Counter.o igor-Coverageerrcounter.o igor-Deletion.o igor-Dinuclmarkov.o igor-Errorscounter.o igor-Errorrate.o igor-ExtractFeatures.o igor-Genechoice.o igor-GenModel.o igor-HypermutationfullNmererrorrate.o igor-Hypermutationglobalerrorrate.o igor-Insertion.o igor-IntStr.o igor-Model_marginals.o igor-Model_Parms.o igor-Pgencounter.o igor-Rec_Event.o igor-Singleerrorrate.o igor-Utils.o igor-main.o -lgsl -lblas -ljemalloc -lpthread -ldl -fopenmp
make[3]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg/igor_src'
make[3]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
dh_auto_test -a
make -j4 check VERBOSE=1
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
Making check in igor_src
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg/igor_src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg/igor_src'
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -a
dh_prep -a
dh_installdirs -a
dh_auto_install -a
make -j1 install DESTDIR=/<<BUILDDIR>>/igor-1.4.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
Making install in igor_src
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg/igor_src'
make[3]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg/igor_src'
/bin/mkdir -p '/<<BUILDDIR>>/igor-1.4.0+dfsg/debian/igor/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c igor '/<<BUILDDIR>>/igor-1.4.0+dfsg/debian/igor/usr/bin'
libtool: install: /usr/bin/install -c igor /<<BUILDDIR>>/igor-1.4.0+dfsg/debian/igor/usr/bin/igor
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg/igor_src'
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg/igor_src'
make[2]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make[3]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
/bin/mkdir -p '/<<BUILDDIR>>/igor-1.4.0+dfsg/debian/igor/usr/bin'
/usr/bin/install -c scripts/igor-compute_pgen '/<<BUILDDIR>>/igor-1.4.0+dfsg/debian/igor/usr/bin'
mkdir -p /<<BUILDDIR>>/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models
cp -r models/* /<<BUILDDIR>>/igor-1.4.0+dfsg/debian/igor/usr/share/igor/models
/bin/mkdir -p '/<<BUILDDIR>>/igor-1.4.0+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-1.4.0+dfsg/debian/igor/usr/share/igor/demo'
make[3]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
mv debian/igor1 debian/igor.1
dh_installman
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
dh_fixperms
find debian -name "*.fasta" -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<BUILDDIR>>/igor-1.4.0+dfsg'
dh_missing -a
dh_dwz -a -a
dh_strip -a -a
dh_makeshlibs -a -a
dh_shlibdeps -a -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 libblas.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 ld-linux-armhf.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_1.4.0+dfsg-2_armhf.deb'.
dpkg-deb: building package 'igor' in '../igor_1.4.0+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../igor_1.4.0+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-08-08T11:54:55Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
igor_1.4.0+dfsg-2_armhf.changes:
--------------------------------
Format: 1.8
Date: Wed, 05 Aug 2020 18:37:57 +0200
Source: igor
Binary: igor igor-dbgsym
Architecture: armhf
Version: 1.4.0+dfsg-2
Distribution: bullseye-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
Closes: 966868
Changes:
igor (1.4.0+dfsg-2) unstable; urgency=medium
.
* Team upload.
* Fix gcc-10 build
Closes: #966868
* debhelper-compat 13 (routine-update)
* Do not use outdated libcblas any more
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Files:
63dbec44192b8b865cc1d810a251b2a5 5792632 debug optional igor-dbgsym_1.4.0+dfsg-2_armhf.deb
2988fc4f90ed57fe31f8045637cb0daf 4730 science optional igor_1.4.0+dfsg-2_armhf.buildinfo
ef4678b6c6e8da6cc3c1f9d8e995473e 486480 science optional igor_1.4.0+dfsg-2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
igor-dbgsym_1.4.0+dfsg-2_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 5792632 bytes: control archive=536 bytes.
369 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: igor-dbgsym
Source: igor
Version: 1.4.0+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5909
Depends: igor (= 1.4.0+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for igor
Build-Ids: 3c2a473bf8c4033335d797250599f65305a84360
drwxr-xr-x root/root 0 2020-08-05 16:37 ./
drwxr-xr-x root/root 0 2020-08-05 16:37 ./usr/
drwxr-xr-x root/root 0 2020-08-05 16:37 ./usr/lib/
drwxr-xr-x root/root 0 2020-08-05 16:37 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-08-05 16:37 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-08-05 16:37 ./usr/lib/debug/.build-id/3c/
-rw-r--r-- root/root 6040528 2020-08-05 16:37 ./usr/lib/debug/.build-id/3c/2a473bf8c4033335d797250599f65305a84360.debug
drwxr-xr-x root/root 0 2020-08-05 16:37 ./usr/share/
drwxr-xr-x root/root 0 2020-08-05 16:37 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-08-05 16:37 ./usr/share/doc/igor-dbgsym -> igor
igor_1.4.0+dfsg-2_armhf.deb
---------------------------
new Debian package, version 2.0.
size 486480 bytes: control archive=2524 bytes.
633 bytes, 13 lines control
7578 bytes, 77 lines md5sums
Package: igor
Version: 1.4.0+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2499
Depends: libblas3 | libblas.so.3, libc6 (>= 2.29), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libgsl25 (>= 2.6), 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.
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Purging /<<BUILDDIR>>
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Build Architecture: armhf
Build-Space: 85252
Build-Time: 508
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 225
Job: igor_1.4.0+dfsg-2
Machine Architecture: armhf
Package: igor
Package-Time: 783
Source-Version: 1.4.0+dfsg-2
Space: 85252
Status: successful
Version: 1.4.0+dfsg-2
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Finished at 2020-08-08T11:54:55Z
Build needed 00:13:03, 85252k disc space