igor →
1.4.0+dfsg-4 →
armhf → 2022-11-11 06:47:50
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| igor 1.4.0+dfsg-4 (armhf) Fri, 11 Nov 2022 06:37:50 +0000 |
+==============================================================================+
Package: igor
Version: 1.4.0+dfsg-4
Source Version: 1.4.0+dfsg-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-5672b47a-6e86-4067-b8da-04c91d782c9b' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/igor-BlBLRR/resolver-X07aHa' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.3 MB]
Fetched 27.7 MB in 13s (2167 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| 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://172.17.4.1/private bookworm-staging/main igor 1.4.0+dfsg-4 (dsc) [2046 B]
Get:2 http://172.17.4.1/private bookworm-staging/main igor 1.4.0+dfsg-4 (tar) [1001 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main igor 1.4.0+dfsg-4 (diff) [5200 B]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/igor-BlBLRR/igor-1.4.0+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/igor-BlBLRR' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev | libblas.so, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
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Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
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Reading package lists...
Reading package lists...
Install main 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:
krb5-locales libpam-cap libperl5.34 perl-modules-5.34
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgsl-dev
libgsl27 libgslcblas0 libicu71 libjemalloc-dev libjemalloc2 libmagic-mgc
libmagic1 libpipeline1 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 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libblas-dev libblas3
libdebhelper-perl libelf1 libfile-stripnondeterminism-perl libgsl-dev
libgsl27 libgslcblas0 libicu71 libjemalloc-dev libjemalloc2 libmagic-mgc
libmagic1 libpipeline1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db po-debconf sbuild-build-depends-main-dummy
0 upgraded, 37 newly installed, 0 to remove and 54 not upgraded.
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Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.0-1 [1299 kB]
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Get:9 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
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Get:13 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
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Get:16 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10.1 [79.9 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10.1 [940 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.1-2 [109 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libblas-dev armhf 3.10.1-2 [114 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libgslcblas0 armhf 2.7.1+dfsg-3 [81.4 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libgsl27 armhf 2.7.1+dfsg-3 [758 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libgsl-dev armhf 2.7.1+dfsg-3 [958 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libjemalloc2 armhf 5.2.1-5+rpi1 [187 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libjemalloc-dev armhf 5.2.1-5+rpi1 [413 kB]
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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
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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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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-2+rpi1 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.3+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1.1 bsdutils_1:2.38.1-1.1 build-essential_12.9 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.10.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblas-dev_3.10.1-2 libblas3_3.10.1-2 libblkid1_2.38.1-1.1 libbz2-1.0_1.0.8-5+b2 libc-bin_2.35-2+rpi1 libc-dev-bin_2.35-2+rpi1 libc6_2.35-2+rpi1 libc6-dev_2.35-2+rpi1 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.10.1 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.8-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgsl-dev_2.7.1+dfsg-3 libgsl27_2.7.1+dfsg-3 libgslcblas0_2.7.1+dfsg-3 libgssapi-krb5-2_1.20-1 libhogweed6_3.8.1-2 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjemalloc-dev_5.2.1-5+rpi1 libjemalloc2_5.2.1-5+rpi1 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.5-0_2.5.13+dfsg-2+rpi1 liblz4-1_1.9.4-1+rpi1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38.1-1.1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-5 libpam-modules-bin_1.5.2-5 libpam-runtime_1.5.2-5 libpam0g_1.5.2-5 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.6-3 libreadline8_8.2-1 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1.1 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssl1.1_1.1.1o-1 libssl3_3.0.5-4 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-4 libsystemd0_251.5-1+rpi1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.5-1+rpi1 libunistring2_1.0-2 libuuid1_2.38.1-1.1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.12.3+dfsg1-1 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.11.0-1 mawk_1.3.4.20200120-3.1 mount_2.38.1-1.1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 passwd_1:4.12.3+dfsg1-1 patch_2.7.6-7 perl_5.36.0-4 perl-base_5.36.0-4 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.31 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-1.1 util-linux-extra_2.38.1-1.1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 3.0 (quilt)
Source: igor
Binary: igor
Architecture: any
Version: 1.4.0+dfsg-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Homepage: https://github.com/qmarcou/IGoR/
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/igor
Vcs-Git: https://salsa.debian.org/med-team/igor.git
Testsuite: autopkgtest
Testsuite-Triggers: build-essential
Build-Depends: debhelper-compat (= 13), libjemalloc-dev, libgsl-dev, libblas-dev | libblas.so
Package-List:
igor deb science optional arch=any
Checksums-Sha1:
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5003386f85287f87d50662fcfb3fe96b9ae0102d 5200 igor_1.4.0+dfsg-4.debian.tar.xz
Checksums-Sha256:
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951c0b83d26b3499481797a85462b52c941b1bb5e3026427744e9a20ac595dfc 5200 igor_1.4.0+dfsg-4.debian.tar.xz
Files:
272f7e96c7aadd4791679d31dadf0f6f 1001484 igor_1.4.0+dfsg.orig.tar.xz
245d7f388afd522f707a0e8cd00b4869 5200 igor_1.4.0+dfsg-4.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.mZeH4XaB/trustedkeys.kbx': General error
gpgv: Signature made Sat Nov 5 19:49:36 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./igor_1.4.0+dfsg-4.dsc
dpkg-source: info: extracting igor in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking igor_1.4.0+dfsg.orig.tar.xz
dpkg-source: info: unpacking igor_1.4.0+dfsg-4.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 disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=79d111ecf76d4d72929efb4c6c309344
JOURNAL_STREAM=8:26624
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-5672b47a-6e86-4067-b8da-04c91d782c9b
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c177701
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package igor
dpkg-buildpackage: info: source version 1.4.0+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
rm -rf docs/latex
rm -rf docs/html
rm -rf config.guess config.sub
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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 race-free 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 the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... 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 file... file
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 for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.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 the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
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 the compiler supports GNU C... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to enable C11 features... (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 _Bool... no
checking for stdbool.h that conforms to C99... yes
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 (/<<PKGBUILDDIR>>/igor_src)
configure: WARNING: no configuration information is in igor_src
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in igor_src
make[3]: Entering directory '/<<PKGBUILDDIR>>/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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Deletion.o `test -f 'Deletion.cpp' || echo './'`Deletion.cpp
Deletion.cpp:1590:44: warning: multi-character character constant [-Wmultichar]
1590 | else if ((*iter)=='14'){
| ^~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/c++/12/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Bestscenarioscounter.h:29,
from Bestscenarioscounter.cpp:26:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_insert_aux(iterator, _Arg&&) [with _Arg = 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> > >; _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++/12/bits/vector.tcc:407:7: 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> > > >::iterator’ changed in GCC 7.1
407 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(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++/12/bits/vector.tcc:439:7: 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> > > >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_emplace_aux(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++/12/bits/vector.tcc:375:7: 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’ changed in GCC 7.1
375 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:395:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<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
395 | _M_insert_aux(begin() + __n, std::move(__tmp._M_val()));
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:398:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<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
398 | _M_realloc_insert(begin() + __n, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_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> > > >]’,
inlined from ‘virtual void Best_scenarios_counter::count_scenario(long double, double, const std::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&)’ at Bestscenarioscounter.cpp:77:41:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<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
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::emplace(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> > > >]’,
inlined from ‘virtual void Best_scenarios_counter::count_scenario(long double, double, const std::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&)’ at Bestscenarioscounter.cpp:84:36:
/usr/include/c++/12/bits/stl_vector.h:1342:32: 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’ changed in GCC 7.1
1342 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::emplace(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> > > >]’,
inlined from ‘virtual void Best_scenarios_counter::count_scenario(long double, double, const std::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&)’ at Bestscenarioscounter.cpp:112:36:
/usr/include/c++/12/bits/stl_vector.h:1342:32: 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’ changed in GCC 7.1
1342 | { 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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Dinuclmarkov.o `test -f 'Dinuclmarkov.cpp' || echo './'`Dinuclmarkov.cpp
Deletion.cpp: In member function ‘virtual void Deletion::iterate(double&, Downstream_scenario_proba_bound_map&, const std::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:909:98: 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:909:98: 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 std::string&, Seq_side)’
69 | std::string operator+(const std::string& , Seq_side );
| ^~~~~~~~
Deletion.cpp:1173:88: 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:1173:88: note: candidate 1: ‘operator+(const char*, int)’ (built-in)
Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Errorscounter.o `test -f 'Errorscounter.cpp' || echo './'`Errorscounter.cpp
Deletion.cpp: In member function ‘virtual bool Deletion::has_effect_on(Seq_type) const’:
Deletion.cpp:1705:2: warning: control reaches end of non-void function [-Wreturn-type]
1705 | }
| ^
In file included from /usr/include/c++/12/bits/stl_algobase.h:71,
from /usr/include/c++/12/bits/forward_list.h:38,
from /usr/include/c++/12/forward_list:38,
from Aligner.h:29,
from Aligner.cpp:27:
/usr/include/c++/12/bits/predefined_ops.h: In function ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Iterator2 = __gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >; _Compare = bool (*)(Alignment_data, Alignment_data)]’:
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
Dinuclmarkov.cpp: In member function ‘virtual void Dinucl_markov::iterate(double&, Downstream_scenario_proba_bound_map&, const std::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:147:95: 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:147:95: 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 std::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:211:95: 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:211:95: note: candidate 1: ‘operator+(const char*, int)’ (built-in)
Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::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:565:95: 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:565:95: note: candidate 1: ‘operator+(const char*, int)’ (built-in)
Utils.h:68:13: note: candidate 2: ‘std::string operator+(const std::string&, Gene_class)’
68 | std::string operator+(const std::string& , Gene_class );
| ^~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from Utils.h:31,
from Aligner.h:37:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
Utils.h: In member function ‘Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]’:
Utils.h:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘Matrix<double> read_substitution_matrix(const std::string&, std::string)’ at Aligner.cpp:1581:25:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {Alignment_data}; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Alignment_data>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {Alignment_data}; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘std::unordered_map<int, std::vector<Alignment_data> > read_alignments_seq_csv(std::string, double, bool)’ at Aligner.cpp:788:38:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/c++/12/queue:61,
from Model_marginals.h:36,
from Counter.h:32,
from Errorscounter.h:29,
from Errorscounter.cpp:26:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(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++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<std::tuple<double, unsigned int, unsigned int> >::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_emplace_aux(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++/12/bits/vector.tcc:375:7: note: parameter passing for argument of type ‘std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator’ changed in GCC 7.1
375 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc:398:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<double, unsigned int, unsigned int>*, std::vector<std::tuple<double, unsigned int, unsigned int> > >’ changed in GCC 7.1
398 | _M_realloc_insert(begin() + __n, std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_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> >]’,
inlined from ‘virtual void Errors_counter::count_scenario(long double, double, const std::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&)’ at Errorscounter.cpp:94:42:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<double, unsigned int, unsigned int>*, std::vector<std::tuple<double, unsigned int, unsigned int> > >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::emplace(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> >]’,
inlined from ‘virtual void Errors_counter::count_scenario(long double, double, const std::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&)’ at Errorscounter.cpp:101:37:
/usr/include/c++/12/bits/stl_vector.h:1342:32: note: parameter passing for argument of type ‘std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator’ changed in GCC 7.1
1342 | { return _M_emplace_aux(__position, std::forward<_Args>(__args)...); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::emplace(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> >]’,
inlined from ‘virtual void Errors_counter::count_scenario(long double, double, const std::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&)’ at Errorscounter.cpp:111:37:
/usr/include/c++/12/bits/stl_vector.h:1342:32: note: parameter passing for argument of type ‘std::vector<std::tuple<double, unsigned int, unsigned int> >::const_iterator’ changed in GCC 7.1
1342 | { 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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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++/12/algorithm:61,
from Aligner.h:35:
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-ExtractFeatures.o `test -f 'ExtractFeatures.cpp' || echo './'`ExtractFeatures.cpp
In file included from /usr/include/c++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’:
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35,
inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/vector.tcc:232:44:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]’ at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘std::__detail::_Hashtable_alloc<_NodeAlloc>::__node_type* std::__detail::_Hashtable_alloc<_NodeAlloc>::_M_allocate_node(_Args&& ...) [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]’ at /usr/include/c++/12/bits/hashtable_policy.h:1968:36:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Genechoice.o `test -f 'Genechoice.cpp' || echo './'`Genechoice.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60:
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Distance = int; _Tp = Alignment_data; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’:
/usr/include/c++/12/bits/stl_algo.h:1625:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1625 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1625:5: 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++/12/bits/stl_algo.h:1625:5: 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++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
In function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’,
inlined from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’ at /usr/include/c++/12/bits/stl_algo.h:1887:34,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’ at /usr/include/c++/12/bits/stl_algo.h:1921:38:
/usr/include/c++/12/bits/stl_algo.h:85:17: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
85 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:87:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
87 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:89:26: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
89 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:94:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
94 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:96:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
96 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’:
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1900:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1900 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = bool (*)(Alignment_data, Alignment_data)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘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> > > >)’ at Aligner.cpp:827:8:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(Alignment_data, Alignment_data)>]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<Alignment_data*, vector<Alignment_data> >; _Compare = bool (*)(Alignment_data, Alignment_data)]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘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> > > >)’ at Aligner.cpp:827:8:
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-GenModel.o `test -f 'GenModel.cpp' || echo './'`GenModel.cpp
Genechoice.cpp: In member function ‘virtual void Gene_choice::iterate(double&, Downstream_scenario_proba_bound_map&, const std::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:908:94: 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:908:94: 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 std::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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-HypermutationfullNmererrorrate.o `test -f 'HypermutationfullNmererrorrate.cpp' || echo './'`HypermutationfullNmererrorrate.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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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++/12/bits/stl_algobase.h:71,
from /usr/include/c++/12/bits/hashtable_policy.h:35,
from /usr/include/c++/12/bits/hashtable.h:35,
from /usr/include/c++/12/unordered_map:46,
from Rec_Event.h:30:
/usr/include/c++/12/bits/predefined_ops.h: In function ‘constexpr bool __gnu_cxx::__ops::_Iter_comp_iter<_Compare>::operator()(_Iterator1, _Iterator2) [with _Iterator1 = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Iterator2 = __gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >; _Compare = D_position_comparator]’:
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >’ changed in GCC 7.1
157 | operator()(_Iterator1 __it1, _Iterator2 __it2)
| ^~~~~~~~
/usr/include/c++/12/bits/predefined_ops.h:157:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >’ changed in GCC 7.1
In file included from /usr/include/c++/12/vector:70,
from Rec_Event.h:32:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(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++/12/bits/vector.tcc:439:7: 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’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
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:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
In file included from /usr/include/c++/12/queue:62,
from Errorrate.h:38:
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from Aligner.h:35,
from Rec_Event.h:41,
from Genechoice.h:29,
from HypermutationfullNmererrorrate.h:31:
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1922:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1844 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1844:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/12/bits/stl_algo.h:1849:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
In file included from /usr/include/c++/12/vector:70,
from Utils.h:31:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘virtual void Hypermutation_full_Nmer_errorrate::update()’ at HypermutationfullNmererrorrate.cpp:961:35:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘virtual void Hypermutation_full_Nmer_errorrate::update()’ at HypermutationfullNmererrorrate.cpp:966:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/algorithm:61,
from Aligner.h:35,
from Rec_Event.h:41:
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<D_position_comparator>]’:
/usr/include/c++/12/bits/stl_algo.h:1782:5: 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
1782 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘virtual void Hypermutation_full_Nmer_errorrate::build_upper_bound_matrix(size_t, size_t)’ at HypermutationfullNmererrorrate.cpp:292:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘virtual void Hypermutation_full_Nmer_errorrate::build_upper_bound_matrix(size_t, size_t)’ at HypermutationfullNmererrorrate.cpp:294:6:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘virtual const double& Hypermutation_full_Nmer_errorrate::get_err_rate_upper_bound(size_t, size_t)’ at HypermutationfullNmererrorrate.cpp:249:27:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’,
inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<double*, vector<double> >]’ at /usr/include/c++/12/bits/stl_algo.h:4820:18,
inlined from ‘virtual const double& Hypermutation_full_Nmer_errorrate::get_err_rate_upper_bound(size_t, size_t)’ at HypermutationfullNmererrorrate.cpp:251:7:
/usr/include/c++/12/bits/stl_algo.h:1937:32: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1940:38: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
1940 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’:
/usr/include/c++/12/bits/stl_algo.h:1802:5: 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
1802 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1802:5: 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++/12/queue:62,
from Rec_Event.h:37:
/usr/include/c++/12/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Distance = int; _Tp = tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’:
/usr/include/c++/12/bits/stl_heap.h:224:5: 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
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from Rec_Event.h:32,
from Model_Parms.h:33,
from GenModel.h:32,
from GenModel.cpp:28:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const Alignment_data&}; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<Alignment_data>::iterator’ changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__heap_select(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’:
/usr/include/c++/12/bits/stl_algo.h:1625:5: 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
1625 | __heap_select(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1625:5: 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++/12/bits/stl_algo.h:1625:5: 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++/12/vector:63:
/usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’:
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]’ at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘std::__detail::_Hashtable_alloc<_NodeAlloc>::__node_type* std::__detail::_Hashtable_alloc<_NodeAlloc>::_M_allocate_node(_Args&& ...) [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]’ at /usr/include/c++/12/bits/hashtable_policy.h:1968:36:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’:
/usr/include/c++/12/bits/stl_algo.h:1908:5: 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
1908 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1908:5: 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 function ‘void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’,
inlined from ‘_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’ at /usr/include/c++/12/bits/stl_algo.h:1887:34,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’ at /usr/include/c++/12/bits/stl_algo.h:1921:38:
/usr/include/c++/12/bits/stl_algo.h:85:17: 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
85 | if (__comp(__a, __b))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:87:21: 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
87 | if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:89:26: 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
89 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:94:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >’ changed in GCC 7.1
94 | else if (__comp(__a, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:96:22: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double>*, std::vector<std::tuple<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int, int, double> > >’ changed in GCC 7.1
96 | else if (__comp(__b, __c))
| ~~~~~~^~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’:
/usr/include/c++/12/bits/stl_algo.h:1922:32: 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
1922 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__partial_sort(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’,
inlined from ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’ at /usr/include/c++/12/bits/stl_algo.h:1916:27:
/usr/include/c++/12/bits/stl_algo.h:1900:25: 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
1900 | std::__heap_select(__first, __middle, __last, __comp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’,
inlined from ‘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)’ at GenModel.cpp:686:64:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/stl_vector.h:1617:35,
inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/vector.tcc:232:44,
inlined from ‘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)’ at GenModel.cpp:689:16:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_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> >]’,
inlined from ‘virtual void Gene_choice::initialize_Len_proba_bound(std::queue<std::shared_ptr<Rec_Event> >&, const Marginal_array_p&, Index_map&)’ at Genechoice.cpp:1360:65:
/usr/include/c++/12/bits/vector.tcc:123:28: 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
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = D_position_comparator]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘virtual void Gene_choice::initialize_Len_proba_bound(std::queue<std::shared_ptr<Rec_Event> >&, const Marginal_array_p&, Index_map&)’ at Genechoice.cpp:1371:10:
/usr/include/c++/12/bits/stl_algo.h:1937:32: 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
1937 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1938 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1939 | __comp);
| ~~~~~~~
In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’,
inlined from ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<D_position_comparator>]’ at /usr/include/c++/12/bits/stl_algo.h:1940:31,
inlined from ‘void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double>*, vector<tuple<__cxx11::basic_string<char, char_traits<char>, allocator<char> >, int, int, double> > >; _Compare = D_position_comparator]’ at /usr/include/c++/12/bits/stl_algo.h:4853:18,
inlined from ‘virtual void Gene_choice::initialize_Len_proba_bound(std::queue<std::shared_ptr<Rec_Event> >&, const Marginal_array_p&, Index_map&)’ at Genechoice.cpp:1371:10:
/usr/include/c++/12/bits/stl_algo.h:1849:32: 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
1849 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_algo.h:1854:30: 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
1854 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Insertion.o `test -f 'Insertion.cpp' || echo './'`Insertion.cpp
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]’ at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘std::__detail::_ReuseOrAllocNode<_NodeAlloc>::__node_type* std::__detail::_ReuseOrAllocNode<_NodeAlloc>::operator()(_Args&& ...) const [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]’ at /usr/include/c++/12/bits/hashtable_policy.h:177:35:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]’ at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘std::__detail::_ReuseOrAllocNode<_NodeAlloc>::__node_type* std::__detail::_ReuseOrAllocNode<_NodeAlloc>::operator()(_Args&& ...) const [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]’ at /usr/include/c++/12/bits/hashtable_policy.h:177:35,
inlined from ‘void std::_Hashtable<_Key, _Value, _Alloc, _ExtractKey, _Equal, _Hash, _RangeHash, _Unused, _RehashPolicy, _Traits>::_M_assign(_Ht&&, const _NodeGenerator&) [with _Ht = const std::_Hashtable<Gene_class, std::pair<const Gene_class, std::vector<Alignment_data> >, std::allocator<std::pair<const Gene_class, std::vector<Alignment_data> > >, std::__detail::_Select1st, std::equal_to<Gene_class>, std::hash<Gene_class>, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, false, true> >&; _NodeGenerator = std::__detail::_ReuseOrAllocNode<std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> > >; _Key = Gene_class; _Value = std::pair<const Gene_class, std::vector<Alignment_data> >; _Alloc = std::allocator<std::pair<const Gene_class, std::vector<Alignment_data> > >; _ExtractKey = std::__detail::_Select1st; _Equal = std::equal_to<Gene_class>; _Hash = std::hash<Gene_class>; _RangeHash = std::__detail::_Mod_range_hashing; _Unused = std::__detail::_Default_ranged_hash; _RehashPolicy = std::__detail::_Prime_rehash_policy; _Traits = std::__detail::_Hashtable_traits<true, false, true>]’ at /usr/include/c++/12/bits/hashtable.h:1357:24:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 std::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:244:93: 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:244:93: 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 std::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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Rec_Event.o `test -f 'Rec_Event.cpp' || echo './'`Rec_Event.cpp
In file included from /usr/include/c++/12/vector:70,
from Rec_Event.h:32,
from Model_Parms.h:33,
from Model_Parms.cpp:30:
/usr/include/c++/12/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’:
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
439 | 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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Singleerrorrate.o `test -f 'Singleerrorrate.cpp' || echo './'`Singleerrorrate.cpp
In file included from Errorrate.h:29,
from Singleerrorrate.h:30,
from Singleerrorrate.cpp:27:
Utils.h: In member function ‘Matrix<T>& Matrix<T>::operator=(const Matrix<T>&) [with T = double]’:
Utils.h:142:9: 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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o igor-Utils.o `test -f 'Utils.cpp' || echo './'`Utils.cpp
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void Model_Parms::read_model_parms(std::string)’ at Model_Parms.cpp:718:32:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void Model_Parms::read_model_parms(std::string)’ at Model_Parms.cpp:721:32:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void Model_Parms::read_model_parms(std::string)’ at Model_Parms.cpp:759:31:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from ‘void Model_Parms::read_model_parms(std::string)’ at Model_Parms.cpp:762:31:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/jemalloc -I/usr/include/gsl -fopenmp -DIGOR_DATA_DIR=\"/usr/share/igor\" -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -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:257:31: warning: ignoring return value of ‘int system(const char*)’ declared with attribute ‘warn_unused_result’ [-Wunused-result]
257 | system(&("man igor")[0]);
| ~~~~~~^~~~~~~~~~~~~~~~~~
main.cpp:289:32: 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:1565:23: 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:1716:23: 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:1750:31: 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:2058:31: 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:2062:39: 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:2068:39: 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:2078:31: 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:142:9: warning: control reaches end of non-void function [-Wreturn-type]
142 | }
| ^
In file included from /usr/include/c++/12/vector:63,
from Rec_Event.h:32:
/usr/include/c++/12/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’:
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >; _ForwardIterator = Alignment_data*; bool _TrivialValueTypes = false]’,
inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*]’ at /usr/include/c++/12/bits/stl_uninitialized.h:185:15,
inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const Alignment_data*, vector<Alignment_data> >; _ForwardIterator = Alignment_data*; _Tp = Alignment_data]’ at /usr/include/c++/12/bits/stl_uninitialized.h:372:37,
inlined from ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = Alignment_data; _Alloc = std::allocator<Alignment_data>]’ at /usr/include/c++/12/bits/stl_vector.h:601:31,
inlined from ‘std::pair<_T1, _T2>::pair(const std::pair<_T1, _T2>&) [with _T1 = const Gene_class; _T2 = std::vector<Alignment_data>]’ at /usr/include/c++/12/bits/stl_pair.h:195:17,
inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/new_allocator.h:175:4,
inlined from ‘static void std::allocator_traits<std::allocator<_Tp1> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = std::pair<const Gene_class, std::vector<Alignment_data> >; _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _Tp = std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true>]’ at /usr/include/c++/12/bits/alloc_traits.h:516:17,
inlined from ‘std::__detail::_Hashtable_alloc<_NodeAlloc>::__node_type* std::__detail::_Hashtable_alloc<_NodeAlloc>::_M_allocate_node(_Args&& ...) [with _Args = {const std::pair<const Gene_class, std::vector<Alignment_data, std::allocator<Alignment_data> > >&}; _NodeAlloc = std::allocator<std::__detail::_Hash_node<std::pair<const Gene_class, std::vector<Alignment_data> >, true> >]’ at /usr/include/c++/12/bits/hashtable_policy.h:1968:36:
/usr/include/c++/12/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const Alignment_data*, std::vector<Alignment_data> >’ changed in GCC 7.1
137 | { return std::__do_uninit_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -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 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -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 '/<<PKGBUILDDIR>>/igor_src'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
make -j4 check "TESTSUITEFLAGS=-j4 --verbose" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making check in igor_src
make[2]: Entering directory '/<<PKGBUILDDIR>>/igor_src'
make[2]: Nothing to be done for 'check'.
make[2]: Leaving directory '/<<PKGBUILDDIR>>/igor_src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_installdirs -a
dh_auto_install --destdir=debian/igor/ -a
make -j1 install DESTDIR=/<<BUILDDIR>>/igor-1.4.0\+dfsg/debian/igor AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in igor_src
make[2]: Entering directory '/<<PKGBUILDDIR>>/igor_src'
make[3]: Entering directory '/<<PKGBUILDDIR>>/igor_src'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/igor/usr/bin'
/bin/bash ../libtool --mode=install /usr/bin/install -c igor '/<<PKGBUILDDIR>>/debian/igor/usr/bin'
libtool: install: /usr/bin/install -c igor /<<PKGBUILDDIR>>/debian/igor/usr/bin/igor
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/igor_src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/igor_src'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/igor/usr/bin'
/usr/bin/install -c scripts/igor-compute_pgen '/<<PKGBUILDDIR>>/debian/igor/usr/bin'
mkdir -p /<<PKGBUILDDIR>>/debian/igor/usr/share/igor/models
cp -r models/* /<<PKGBUILDDIR>>/debian/igor/usr/share/igor/models
/bin/mkdir -p '/<<PKGBUILDDIR>>/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 '/<<PKGBUILDDIR>>/debian/igor/usr/share/igor/demo'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
mv debian/igor1 debian/igor.1
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_fixperms
find debian -name "*.fasta" -exec chmod -x \{\} \;
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/igor/usr/bin/igor contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/igor/usr/bin/igor was not linked against 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' in '../igor_1.4.0+dfsg-4_armhf.deb'.
dpkg-deb: building package 'igor-dbgsym' in '../igor-dbgsym_1.4.0+dfsg-4_armhf.deb'.
dpkg-genbuildinfo --build=any -O../igor_1.4.0+dfsg-4_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../igor_1.4.0+dfsg-4_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-11-11T06:47:41Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
igor_1.4.0+dfsg-4_armhf.changes:
--------------------------------
Format: 1.8
Date: Sat, 05 Nov 2022 20:40:47 +0100
Source: igor
Binary: igor igor-dbgsym
Architecture: armhf
Version: 1.4.0+dfsg-4
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
igor - infers V(D)J recombination processes from sequencing data
Changes:
igor (1.4.0+dfsg-4) unstable; urgency=medium
.
* Team upload.
* Fix watch file
* Standards-Version: 4.6.1 (routine-update)
* lintian-overrides (see lintian bug #1017966)
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8533e82131e4a6565fb5ed80ca033e428c33bcf305a663550cc9e56227dea703 5139 igor_1.4.0+dfsg-4_armhf.buildinfo
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Files:
616f2562a6c6f30b2e2c826d415e5229 5820752 debug optional igor-dbgsym_1.4.0+dfsg-4_armhf.deb
76b1b70ea1f748251fa889241bd16985 5139 science optional igor_1.4.0+dfsg-4_armhf.buildinfo
90b411d7dffdc66b405e6c4a8553154a 494248 science optional igor_1.4.0+dfsg-4_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: igor
Binary: igor igor-dbgsym
Architecture: armhf
Version: 1.4.0+dfsg-4
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Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Fri, 11 Nov 2022 06:47:40 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.71-2),
automake (= 1:1.16.5-1.3),
autopoint (= 0.21-9),
autotools-dev (= 20220109.1),
base-files (= 12.3+rpi1),
base-passwd (= 3.6.1),
bash (= 5.2~rc2-2),
binutils (= 2.39-6+rpi1),
binutils-arm-linux-gnueabihf (= 2.39-6+rpi1),
binutils-common (= 2.39-6+rpi1),
bsdextrautils (= 2.38.1-1.1),
bsdutils (= 1:2.38.1-1.1),
build-essential (= 12.9),
bzip2 (= 1.0.8-5+b2),
coreutils (= 9.1-1),
cpp (= 4:12.2.0-1+rpi1),
cpp-12 (= 12.2.0-3+rpi1),
dash (= 0.5.11+git20210903+057cd650a4ed-9),
debconf (= 1.5.79),
debhelper (= 13.10.1),
debianutils (= 5.7-0.3),
dh-autoreconf (= 20),
dh-strip-nondeterminism (= 1.13.0-1),
diffutils (= 1:3.8-1),
dpkg (= 1.21.9+rpi1),
dpkg-dev (= 1.21.9+rpi1),
dwz (= 0.14+20220924-2),
file (= 1:5.41-4),
findutils (= 4.9.0-3),
g++ (= 4:12.2.0-1+rpi1),
g++-12 (= 12.2.0-3+rpi1),
gcc (= 4:12.2.0-1+rpi1),
gcc-12 (= 12.2.0-3+rpi1),
gcc-12-base (= 12.2.0-3+rpi1),
gettext (= 0.21-9),
gettext-base (= 0.21-9),
grep (= 3.7-1),
groff-base (= 1.22.4-8),
gzip (= 1.12-1),
hostname (= 3.23),
init-system-helpers (= 1.64),
intltool-debian (= 0.35.0+20060710.6),
libacl1 (= 2.3.1-1),
libarchive-zip-perl (= 1.68-1),
libasan8 (= 12.2.0-3+rpi1),
libatomic1 (= 12.2.0-3+rpi1),
libattr1 (= 1:2.5.1-1),
libaudit-common (= 1:3.0.7-1.1),
libaudit1 (= 1:3.0.7-1.1),
libbinutils (= 2.39-6+rpi1),
libblas-dev (= 3.10.1-2),
libblas3 (= 3.10.1-2),
libblkid1 (= 2.38.1-1.1),
libbz2-1.0 (= 1.0.8-5+b2),
libc-bin (= 2.35-2+rpi1),
libc-dev-bin (= 2.35-2+rpi1),
libc6 (= 2.35-2+rpi1),
libc6-dev (= 2.35-2+rpi1),
libcap-ng0 (= 0.8.3-1),
libcap2 (= 1:2.44-1),
libcc1-0 (= 12.2.0-3+rpi1),
libcom-err2 (= 1.46.6~rc1-1),
libcrypt-dev (= 1:4.4.28-2),
libcrypt1 (= 1:4.4.28-2),
libctf-nobfd0 (= 2.39-6+rpi1),
libctf0 (= 2.39-6+rpi1),
libdb5.3 (= 5.3.28+dfsg1-0.10),
libdebconfclient0 (= 0.264),
libdebhelper-perl (= 13.10.1),
libdpkg-perl (= 1.21.9+rpi1),
libelf1 (= 0.187-2+rpi2),
libfile-stripnondeterminism-perl (= 1.13.0-1),
libgcc-12-dev (= 12.2.0-3+rpi1),
libgcc-s1 (= 12.2.0-3+rpi1),
libgcrypt20 (= 1.10.1-2+b2),
libgdbm-compat4 (= 1.23-3),
libgdbm6 (= 1.23-3),
libgmp10 (= 2:6.2.1+dfsg1-1.1),
libgomp1 (= 12.2.0-3+rpi1),
libgpg-error0 (= 1.45-2),
libgsl-dev (= 2.7.1+dfsg-3),
libgsl27 (= 2.7.1+dfsg-3),
libgslcblas0 (= 2.7.1+dfsg-3),
libgssapi-krb5-2 (= 1.20-1),
libicu71 (= 71.1-3),
libisl23 (= 0.25-1),
libjemalloc-dev (= 5.2.1-5+rpi1),
libjemalloc2 (= 5.2.1-5+rpi1),
libk5crypto3 (= 1.20-1),
libkeyutils1 (= 1.6.3-1),
libkrb5-3 (= 1.20-1),
libkrb5support0 (= 1.20-1),
liblz4-1 (= 1.9.4-1+rpi1),
liblzma5 (= 5.2.5-2.1),
libmagic-mgc (= 1:5.41-4),
libmagic1 (= 1:5.41-4),
libmount1 (= 2.38.1-1.1),
libmpc3 (= 1.2.1-2),
libmpfr6 (= 4.1.0-3),
libnsl-dev (= 1.3.0-2),
libnsl2 (= 1.3.0-2),
libpam-modules (= 1.5.2-5),
libpam-modules-bin (= 1.5.2-5),
libpam-runtime (= 1.5.2-5),
libpam0g (= 1.5.2-5),
libpcre2-8-0 (= 10.40-1+b2),
libpcre3 (= 2:8.39-14),
libperl5.36 (= 5.36.0-4),
libpipeline1 (= 1.5.6-3),
libseccomp2 (= 2.5.4-1+rpi1),
libselinux1 (= 3.4-1),
libsmartcols1 (= 2.38.1-1.1),
libssl3 (= 3.0.5-4),
libstdc++-12-dev (= 12.2.0-3+rpi1),
libstdc++6 (= 12.2.0-3+rpi1),
libsub-override-perl (= 0.09-4),
libsystemd0 (= 251.5-1+rpi1),
libtinfo6 (= 6.3+20220423-2),
libtirpc-common (= 1.3.3+ds-1),
libtirpc-dev (= 1.3.3+ds-1),
libtirpc3 (= 1.3.3+ds-1),
libtool (= 2.4.7-4),
libubsan1 (= 12.2.0-3+rpi1),
libuchardet0 (= 0.0.7-1),
libudev1 (= 251.5-1+rpi1),
libunistring2 (= 1.0-2),
libuuid1 (= 2.38.1-1.1),
libxml2 (= 2.9.14+dfsg-1),
libzstd1 (= 1.5.2+dfsg-1),
linux-libc-dev (= 5.19.6-1+rpi1),
login (= 1:4.12.3+dfsg1-1),
m4 (= 1.4.19-1),
make (= 4.3-4.1),
man-db (= 2.11.0-1),
mawk (= 1.3.4.20200120-3.1),
ncurses-base (= 6.3+20220423-2),
ncurses-bin (= 6.3+20220423-2),
patch (= 2.7.6-7),
perl (= 5.36.0-4),
perl-base (= 5.36.0-4),
perl-modules-5.36 (= 5.36.0-4),
po-debconf (= 1.0.21+nmu1),
rpcsvc-proto (= 1.4.2-4),
sed (= 4.8-1),
sensible-utils (= 0.0.17),
sgml-base (= 1.31),
sysvinit-utils (= 3.05-6),
tar (= 1.34+dfsg-1),
util-linux (= 2.38.1-1.1),
util-linux-extra (= 2.38.1-1.1),
xz-utils (= 5.2.5-2.1),
zlib1g (= 1:1.2.11.dfsg-4.1)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="C.UTF-8"
SOURCE_DATE_EPOCH="1667677247"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
igor-dbgsym_1.4.0+dfsg-4_armhf.deb
----------------------------------
new Debian package, version 2.0.
size 5820752 bytes: control archive=540 bytes.
369 bytes, 12 lines control
106 bytes, 1 lines md5sums
Package: igor-dbgsym
Source: igor
Version: 1.4.0+dfsg-4
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 5886
Depends: igor (= 1.4.0+dfsg-4)
Section: debug
Priority: optional
Description: debug symbols for igor
Build-Ids: e1d580d301272964a1c43cf1c8772fe7ff5aa068
drwxr-xr-x root/root 0 2022-11-05 19:40 ./
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/lib/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/lib/debug/.build-id/e1/
-rw-r--r-- root/root 6016760 2022-11-05 19:40 ./usr/lib/debug/.build-id/e1/d580d301272964a1c43cf1c8772fe7ff5aa068.debug
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-11-05 19:40 ./usr/share/doc/igor-dbgsym -> igor
igor_1.4.0+dfsg-4_armhf.deb
---------------------------
new Debian package, version 2.0.
size 494248 bytes: control archive=2528 bytes.
634 bytes, 13 lines control
7578 bytes, 77 lines md5sums
Package: igor
Version: 1.4.0+dfsg-4
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2555
Depends: libblas3 | libblas.so.3, libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libgsl27 (>= 2.7.1), libjemalloc2 (>= 5.0.0), libstdc++6 (>= 11)
Section: science
Priority: optional
Homepage: https://github.com/qmarcou/IGoR/
Description: infers V(D)J recombination processes from sequencing data
IGoR (Inference and Generation of Repertoires) is a versatile software
to analyze and model immune receptors generation, selection, mutation
and all other processes.
drwxr-xr-x root/root 0 2022-11-05 19:40 ./
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/bin/
-rwxr-xr-x root/root 787976 2022-11-05 19:40 ./usr/bin/igor
-rwxr-xr-x root/root 906 2022-11-05 19:40 ./usr/bin/igor-compute_pgen
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/doc/igor/
-rw-r--r-- root/root 850 2022-11-05 19:40 ./usr/share/doc/igor/changelog.Debian.gz
-rw-r--r-- root/root 1271 2020-04-11 17:57 ./usr/share/doc/igor/changelog.gz
-rw-r--r-- root/root 1147 2022-11-05 19:40 ./usr/share/doc/igor/copyright
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/doc/igor/examples/
-rw-r--r-- root/root 84 2020-04-11 17:57 ./usr/share/doc/igor/examples/genomicDs.fasta
-rw-r--r-- root/root 2022 2020-04-11 17:57 ./usr/share/doc/igor/examples/genomicJs_all_curated.fasta
-rw-r--r-- root/root 33856 2020-04-11 17:57 ./usr/share/doc/igor/examples/genomicVs_with_primers.fasta
-rw-r--r-- root/root 18300 2020-04-11 17:57 ./usr/share/doc/igor/examples/murugan_naive1_noncoding_demo_seqs.txt
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/demo/
-rw-r--r-- root/root 84 2022-11-05 19:40 ./usr/share/igor/demo/genomicDs.fasta
-rw-r--r-- root/root 2022 2022-11-05 19:40 ./usr/share/igor/demo/genomicJs_all_curated.fasta
-rw-r--r-- root/root 33856 2022-11-05 19:40 ./usr/share/igor/demo/genomicVs_with_primers.fasta
-rw-r--r-- root/root 18300 2022-11-05 19:40 ./usr/share/igor/demo/murugan_naive1_noncoding_demo_seqs.txt
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/
-rw-r--r-- root/root 690 2022-11-05 19:40 ./usr/share/igor/models/heavy_pen_substitution_matrix.csv
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/models/
-rw-r--r-- root/root 18959 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/models/model_marginals.txt
-rw-r--r-- root/root 20986 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/models/model_parms.txt
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/ref_genome/
-rw-r--r-- root/root 117 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/ref_genome/J_gene_CDR3_anchors.csv
-rw-r--r-- root/root 1044 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/ref_genome/V_gene_CDR3_anchors.csv
-rw-r--r-- root/root 444 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 19475 2022-11-05 19:40 ./usr/share/igor/models/human/IGK/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/IGL/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/IGL/models/
-rw-r--r-- root/root 17632 2022-11-05 19:40 ./usr/share/igor/models/human/IGL/models/model_marginals.txt
-rw-r--r-- root/root 23091 2022-11-05 19:40 ./usr/share/igor/models/human/IGL/models/model_parms.txt
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/IGL/ref_genome/
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-rw-r--r-- root/root 1117 2022-11-05 19:40 ./usr/share/igor/models/human/IGL/ref_genome/V_gene_CDR3_anchors.csv
-rw-r--r-- root/root 343 2022-11-05 19:40 ./usr/share/igor/models/human/IGL/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 21688 2022-11-05 19:40 ./usr/share/igor/models/human/IGL/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/
-rw-r--r-- root/root 523 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/model.info
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/models/
-rw-r--r-- root/root 483313 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/models/model_marginals.txt
-rw-r--r-- root/root 35291 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/models/model_parms.txt
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/ref_genome/
-rw-r--r-- root/root 102 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/ref_genome/J_gene_CDR3_anchors.csv
-rw-r--r-- root/root 1151 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/ref_genome/V_gene_CDR3_anchors.csv
-rw-r--r-- root/root 1335 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/ref_genome/genomicDs.fasta
-rw-r--r-- root/root 464 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 30236 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/
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-rw-r--r-- root/root 35514 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_5mer_J_hyperm_parms.txt
-rw-r--r-- root/root 35517 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_5mer_V_hyperm_parms.txt
-rw-r--r-- root/root 35599 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_7mer_D_hyperm_parms.txt
-rw-r--r-- root/root 35597 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_7mer_J_hyperm_parms.txt
-rw-r--r-- root/root 35599 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_7mer_V_hyperm_parms.txt
-rw-r--r-- root/root 35684 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_9mer_D_hyperm_parms.txt
-rw-r--r-- root/root 35672 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_9mer_J_hyperm_parms.txt
-rw-r--r-- root/root 35679 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/ind_9mer_V_hyperm_parms.txt
-rw-r--r-- root/root 48 2022-11-05 19:40 ./usr/share/igor/models/human/bcr_heavy/supplementary_models/models.info
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_alpha/
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drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_alpha/ref_genome/
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-rw-r--r-- root/root 4983 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_alpha/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 29702 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_alpha/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/
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drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/models/
-rw-r--r-- root/root 114449 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/models/model_marginals.txt
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drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/ref_genome/
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-rw-r--r-- root/root 33856 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/supplementary_models/
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-rw-r--r-- root/root 38249 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_1/final_parms.txt
-rw-r--r-- root/root 35 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_1/model.info
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_4/
-rw-r--r-- root/root 33314 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_4/final_marginals.txt
-rw-r--r-- root/root 38249 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_4/final_parms.txt
-rw-r--r-- root/root 35 2022-11-05 19:40 ./usr/share/igor/models/human/tcr_beta/supplementary_models/naive_4/model.info
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/mouse/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/
-rw-r--r-- root/root 436 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/model.info
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/models/
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-rw-r--r-- root/root 13475 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/models/model_parms.txt
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/
-rw-r--r-- root/root 257 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/J_gene_CDR3_anchors.csv
-rw-r--r-- root/root 448 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/V_gene_CDR3_anchors.csv
-rw-r--r-- root/root 48 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/genomicDs.fasta
-rw-r--r-- root/root 871 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/genomicJs.fasta
-rw-r--r-- root/root 10417 2022-11-05 19:40 ./usr/share/igor/models/mouse/tcr_beta/ref_genome/genomicVs.fasta
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/man/
drwxr-xr-x root/root 0 2022-11-05 19:40 ./usr/share/man/man1/
-rw-r--r-- root/root 374 2022-11-05 19:40 ./usr/share/man/man1/igor.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 74836
Build-Time: 262
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 296
Job: igor_1.4.0+dfsg-4
Machine Architecture: armhf
Package: igor
Package-Time: 591
Source-Version: 1.4.0+dfsg-4
Space: 74836
Status: successful
Version: 1.4.0+dfsg-4
--------------------------------------------------------------------------------
Finished at 2022-11-11T06:47:41Z
Build needed 00:09:51, 74836k disk space