idba →
1.1.3-8 →
armhf → 2022-11-08 08:02:25
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| idba 1.1.3-8 (armhf) Tue, 08 Nov 2022 07:30:03 +0000 |
+==============================================================================+
Package: idba
Version: 1.1.3-8
Source Version: 1.1.3-8
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-deb14a57-64ea-4f5f-a4d5-d830d13b7bf1' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| 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 [14.2 MB]
Fetched 27.7 MB in 30s (907 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: 'idba' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/idba.git
Please use:
git clone https://salsa.debian.org/med-team/idba.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 711 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main idba 1.1.3-8 (dsc) [2022 B]
Get:2 http://172.17.4.1/private bookworm-staging/main idba 1.1.3-8 (tar) [446 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main idba 1.1.3-8 (diff) [263 kB]
Fetched 711 kB in 0s (3850 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/idba-JfD44p/idba-1.1.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/idba-JfD44p' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-IIpQzw/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-IIpQzw/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-IIpQzw/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (1827 B/s)
Reading package lists...
W: copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap libperl5.34 netbase perl-modules-5.34 sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 40 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.6 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14767 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libgtest-dev, python3
Filtered Build-Depends: debhelper-compat (= 13), libgtest-dev, python3
dpkg-deb: building package 'sbuild-build-depends-idba-dummy' in '/<<BUILDDIR>>/resolver-IIpQzw/apt_archive/sbuild-build-depends-idba-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-idba-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Sources [515 B]
Get:5 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Packages [580 B]
Fetched 2428 B in 1s (2142 B/s)
Reading package lists...
W: copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
Reading package lists...
Install idba build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap libperl5.34 netbase 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
googletest groff-base intltool-debian libarchive-zip-perl libdebhelper-perl
libelf1 libexpat1 libfile-stripnondeterminism-perl libgtest-dev libicu71
libmagic-mgc libmagic1 libmpdec3 libpipeline1 libpython3-stdlib
libpython3.10-minimal libpython3.10-stdlib libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db media-types po-debconf python3
python3-minimal python3.10 python3.10-minimal
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl python3-doc python3-tk python3-venv python3.10-venv
python3.10-doc binfmt-support
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
googletest groff-base intltool-debian libarchive-zip-perl libdebhelper-perl
libelf1 libexpat1 libfile-stripnondeterminism-perl libgtest-dev libicu71
libmagic-mgc libmagic1 libmpdec3 libpipeline1 libpython3-stdlib
libpython3.10-minimal libpython3.10-stdlib libsub-override-perl libtool
libuchardet0 libxml2 m4 man-db media-types po-debconf python3
python3-minimal python3.10 python3.10-minimal
sbuild-build-depends-idba-dummy
0 upgraded, 42 newly installed, 0 to remove and 40 not upgraded.
Need to get 23.2 MB of archives.
After this operation, 95.5 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-IIpQzw/apt_archive ./ sbuild-build-depends-idba-dummy 0.invalid.0 [876 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-minimal armhf 3.10.8-1 [768 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.5.0-1 [77.2 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf python3.10-minimal armhf 3.10.8-1 [1476 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.10.6-1 [38.7 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf media-types all 8.0.0 [33.4 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libpython3.10-stdlib armhf 3.10.8-1 [1597 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf python3.10 armhf 3.10.8-1 [505 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.10.6-1 [21.7 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.10.6-1 [38.2 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1.1 [78.2 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.11.0-1 [1299 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.10.1 [79.9 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.10.1 [940 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf googletest all 1.12.1-0.2 [506 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libgtest-dev armhf 1.12.1-0.2 [230 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up autoconf (2.71-2) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-9) ...
Setting up libgtest-dev:armhf (1.12.1-0.2) ...
Setting up libtool (2.4.7-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libpython3.10-stdlib:armhf (3.10.8-1) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14+20220924-2) ...
Setting up groff-base (1.22.4-8) ...
Setting up libpython3-stdlib:armhf (3.10.6-1) ...
Setting up python3.10 (3.10.8-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.10.6-1) ...
Setting up man-db (2.11.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.10.1) ...
Setting up sbuild-build-depends-idba-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.35-2+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp 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 googletest_1.12.1-0.2 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 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 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 libexpat1_2.5.0-1 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 libgssapi-krb5-2_1.20-1 libgtest-dev_1.12.1-0.2 libhogweed6_3.8.1-2 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 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 libmpdec3_2.5.1-2+rpi1 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 libperl5.34_5.34.0-5 libperl5.36_5.36.0-4 libpipeline1_1.5.6-3 libpython3-stdlib_3.10.6-1 libpython3.10-minimal_3.10.8-1 libpython3.10-stdlib_3.10.8-1 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 media-types_8.0.0 mount_2.38.1-1.1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 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-5.34_5.34.0-5 perl-modules-5.36_5.36.0-4 pinentry-curses_1.2.0-2 po-debconf_1.0.21+nmu1 python3_3.10.6-1 python3-minimal_3.10.6-1 python3.10_3.10.8-1 python3.10-minimal_3.10.8-1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-idba-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
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.fnKBqxrj/trustedkeys.kbx': General error
gpgv: Signature made Sat Nov 5 20:30:52 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 ./idba_1.1.3-8.dsc
dpkg-source: info: extracting idba in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking idba_1.1.3.orig.tar.gz
dpkg-source: info: unpacking idba_1.1.3-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying install_all_idba_flavours.patch
dpkg-source: info: applying use-atomic-for-mips.patch
dpkg-source: info: applying spelling.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying use_debian_packaged_googletest.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-deb14a57-64ea-4f5f-a4d5-d830d13b7bf1
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package idba
dpkg-buildpackage: info: source version 1.1.3-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:7: warning: The macro `AC_CONFIG_HEADER' is obsolete.
configure.ac:7: You should run autoupdate.
./lib/autoconf/status.m4:719: AC_CONFIG_HEADER is expanded from...
configure.ac:7: the top level
configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated.
./lib/autoconf/general.m4:2434: AC_DIAGNOSE is expanded from...
aclocal.m4:429: AM_INIT_AUTOMAKE is expanded from...
configure.ac:8: the top level
configure.ac:30: warning: AC_OUTPUT should be used without arguments.
configure.ac:30: You should run autoupdate.
configure.ac:8: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.ac:8: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
bin/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
bin/Makefile.am:9: warning: source file '$(top_srcdir)/src/tools/fa2fq.cpp' is in a subdirectory,
bin/Makefile.am:9: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least one source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However, this
automake: behavior may change in a future Automake major version, with object
automake: files being placed in the same subdirectory as the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
bin/Makefile.am:19: warning: source file '$(top_srcdir)/src/tools/filter_blat.cpp' is in a subdirectory,
bin/Makefile.am:19: but option 'subdir-objects' is disabled
bin/Makefile.am:17: warning: source file '$(top_srcdir)/src/tools/filter_contigs.cpp' is in a subdirectory,
bin/Makefile.am:17: but option 'subdir-objects' is disabled
bin/Makefile.am:33: warning: source file '$(top_srcdir)/src/release/filterfa.cpp' is in a subdirectory,
bin/Makefile.am:33: but option 'subdir-objects' is disabled
bin/Makefile.am:25: warning: source file '$(top_srcdir)/src/release/fq2fa.cpp' is in a subdirectory,
bin/Makefile.am:25: but option 'subdir-objects' is disabled
bin/Makefile.am:34: warning: source file '$(top_srcdir)/src/release/idba.cpp' is in a subdirectory,
bin/Makefile.am:34: but option 'subdir-objects' is disabled
bin/Makefile.am:30: warning: source file '$(top_srcdir)/src/release/idba_hybrid.cpp' is in a subdirectory,
bin/Makefile.am:30: but option 'subdir-objects' is disabled
bin/Makefile.am:29: warning: source file '$(top_srcdir)/src/release/idba_tran.cpp' is in a subdirectory,
bin/Makefile.am:29: but option 'subdir-objects' is disabled
bin/Makefile.am:13: warning: source file '$(top_srcdir)/src/tools/idba_tran_test.cpp' is in a subdirectory,
bin/Makefile.am:13: but option 'subdir-objects' is disabled
bin/Makefile.am:27: warning: source file '$(top_srcdir)/src/release/idba_ud.cpp' is in a subdirectory,
bin/Makefile.am:27: but option 'subdir-objects' is disabled
bin/Makefile.am:31: warning: source file '$(top_srcdir)/src/release/parallel_blat.cpp' is in a subdirectory,
bin/Makefile.am:31: but option 'subdir-objects' is disabled
bin/Makefile.am:18: warning: source file '$(top_srcdir)/src/tools/parallel_rna_blat.cpp' is in a subdirectory,
bin/Makefile.am:18: but option 'subdir-objects' is disabled
bin/Makefile.am:12: warning: source file '$(top_srcdir)/src/tools/print_graph.cpp' is in a subdirectory,
bin/Makefile.am:12: but option 'subdir-objects' is disabled
bin/Makefile.am:28: warning: source file '$(top_srcdir)/src/release/raw_n50.cpp' is in a subdirectory,
bin/Makefile.am:28: but option 'subdir-objects' is disabled
bin/Makefile.am:14: warning: source file '$(top_srcdir)/src/tools/sample_reads.cpp' is in a subdirectory,
bin/Makefile.am:14: but option 'subdir-objects' is disabled
bin/Makefile.am:7: warning: source file '$(top_srcdir)/src/tools/scaffold.cpp' is in a subdirectory,
bin/Makefile.am:7: but option 'subdir-objects' is disabled
bin/Makefile.am:6: warning: source file '$(top_srcdir)/src/tools/shuffle_reads.cpp' is in a subdirectory,
bin/Makefile.am:6: but option 'subdir-objects' is disabled
bin/Makefile.am:36: warning: source file '$(top_srcdir)/src/release/sim_reads.cpp' is in a subdirectory,
bin/Makefile.am:36: but option 'subdir-objects' is disabled
bin/Makefile.am:32: warning: source file '$(top_srcdir)/src/release/sim_reads_tran.cpp' is in a subdirectory,
bin/Makefile.am:32: but option 'subdir-objects' is disabled
bin/Makefile.am:15: warning: source file '$(top_srcdir)/src/tools/sort_psl.cpp' is in a subdirectory,
bin/Makefile.am:15: but option 'subdir-objects' is disabled
bin/Makefile.am:16: warning: source file '$(top_srcdir)/src/tools/sort_reads.cpp' is in a subdirectory,
bin/Makefile.am:16: but option 'subdir-objects' is disabled
bin/Makefile.am:20: warning: source file '$(top_srcdir)/src/tools/split_fa.cpp' is in a subdirectory,
bin/Makefile.am:20: but option 'subdir-objects' is disabled
bin/Makefile.am:23: warning: source file '$(top_srcdir)/src/tools/split_fq.cpp' is in a subdirectory,
bin/Makefile.am:23: but option 'subdir-objects' is disabled
bin/Makefile.am:35: warning: source file '$(top_srcdir)/src/release/split_scaffold.cpp' is in a subdirectory,
bin/Makefile.am:35: but option 'subdir-objects' is disabled
bin/Makefile.am:21: warning: source file '$(top_srcdir)/src/tools/test.cpp' is in a subdirectory,
bin/Makefile.am:21: but option 'subdir-objects' is disabled
bin/Makefile.am:8: warning: source file '$(top_srcdir)/src/tools/validate_component.cpp' is in a subdirectory,
bin/Makefile.am:8: but option 'subdir-objects' is disabled
bin/Makefile.am:26: warning: source file '$(top_srcdir)/src/release/validate_contigs_blat.cpp' is in a subdirectory,
bin/Makefile.am:26: but option 'subdir-objects' is disabled
bin/Makefile.am:11: warning: source file '$(top_srcdir)/src/tools/validate_contigs_mummer.cpp' is in a subdirectory,
bin/Makefile.am:11: but option 'subdir-objects' is disabled
bin/Makefile.am:22: warning: source file '$(top_srcdir)/src/tools/validate_reads_blat.cpp' is in a subdirectory,
bin/Makefile.am:22: but option 'subdir-objects' is disabled
bin/Makefile.am:10: warning: source file '$(top_srcdir)/src/tools/validate_rna.cpp' is in a subdirectory,
bin/Makefile.am:10: but option 'subdir-objects' is disabled
lib/Makefile.am:3: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/basic/math.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/hash_aligner.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/options_description.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/log.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/utils.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/misc/blat_record.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/short_sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_reader.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_writer.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence_io.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/sequence/compact_sequence.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph_branch_group.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/scaffold_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_graph.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/hash_graph_branch_group.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/graph/contig_info.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/local_assembler.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:5: warning: source file '$(top_srcdir)/src/assembly/assembly_utility.cpp' is in a subdirectory,
lib/Makefile.am:5: but option 'subdir-objects' is disabled
lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
lib/Makefile.am:68: but option 'subdir-objects' is disabled
lib/Makefile.am:68: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest-all.cc' is in a subdirectory,
lib/Makefile.am:68: but option 'subdir-objects' is disabled
test/Makefile.am:4: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
test/Makefile.am:11: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:11: but option 'subdir-objects' is disabled
test/Makefile.am:11: warning: source file '$(top_srcdir)/src/test/atomic_integer_unittest.cpp' is in a subdirectory,
test/Makefile.am:11: but option 'subdir-objects' is disabled
test/Makefile.am:8: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:8: but option 'subdir-objects' is disabled
test/Makefile.am:8: warning: source file '$(top_srcdir)/src/test/bit_edges_unittest.cpp' is in a subdirectory,
test/Makefile.am:8: but option 'subdir-objects' is disabled
test/Makefile.am:6: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:6: but option 'subdir-objects' is disabled
test/Makefile.am:6: warning: source file '$(top_srcdir)/src/test/compact_sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:6: but option 'subdir-objects' is disabled
test/Makefile.am:17: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:17: but option 'subdir-objects' is disabled
test/Makefile.am:17: warning: source file '$(top_srcdir)/src/test/hash_map_unittest.cpp' is in a subdirectory,
test/Makefile.am:17: but option 'subdir-objects' is disabled
test/Makefile.am:10: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:10: but option 'subdir-objects' is disabled
test/Makefile.am:10: warning: source file '$(top_srcdir)/src/test/hash_set_unittest.cpp' is in a subdirectory,
test/Makefile.am:10: but option 'subdir-objects' is disabled
test/Makefile.am:7: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
test/Makefile.am:7: warning: source file '$(top_srcdir)/src/test/hash_table_unittest.cpp' is in a subdirectory,
test/Makefile.am:7: but option 'subdir-objects' is disabled
test/Makefile.am:13: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:13: but option 'subdir-objects' is disabled
test/Makefile.am:13: warning: source file '$(top_srcdir)/src/test/histgram_unittest.cpp' is in a subdirectory,
test/Makefile.am:13: but option 'subdir-objects' is disabled
test/Makefile.am:9: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:9: but option 'subdir-objects' is disabled
test/Makefile.am:9: warning: source file '$(top_srcdir)/src/test/kmer_unittest.cpp' is in a subdirectory,
test/Makefile.am:9: but option 'subdir-objects' is disabled
test/Makefile.am:14: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:14: but option 'subdir-objects' is disabled
test/Makefile.am:14: warning: source file '$(top_srcdir)/src/test/managed_list_unittest.cpp' is in a subdirectory,
test/Makefile.am:14: but option 'subdir-objects' is disabled
test/Makefile.am:15: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:15: but option 'subdir-objects' is disabled
test/Makefile.am:15: warning: source file '$(top_srcdir)/src/test/sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:15: but option 'subdir-objects' is disabled
test/Makefile.am:16: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:16: but option 'subdir-objects' is disabled
test/Makefile.am:16: warning: source file '$(top_srcdir)/src/test/short_sequence_unittest.cpp' is in a subdirectory,
test/Makefile.am:16: but option 'subdir-objects' is disabled
test/Makefile.am:12: warning: source file '$(top_srcdir)/gtest_src/gtest/gtest_main.cc' is in a subdirectory,
test/Makefile.am:12: but option 'subdir-objects' is disabled
test/Makefile.am:12: warning: source file '$(top_srcdir)/src/test/vertex_status_unittest.cpp' is in a subdirectory,
test/Makefile.am:12: but option 'subdir-objects' is disabled
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_configure -- LDFLAGS="-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" LIBS=" -latomic"
./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 "LDFLAGS=-Wl,-z,relro -Wl,-z,now -Wl,--as-needed" "LIBS= -latomic"
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 for g++... g++
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 g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
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 ranlib... ranlib
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 _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for an ANSI C-conforming const... yes
checking for working memcmp... yes
checking for vprintf... yes
checking for sqrt... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating bin/Makefile
config.status: creating lib/Makefile
config.status: creating test/Makefile
config.status: creating script/Makefile
config.status: creating config.h
config.status: executing depfiles commands
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in lib
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o math.o `test -f '../src/basic/math.cpp' || echo './'`../src/basic/math.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_aligner.o `test -f '../src/misc/hash_aligner.cpp' || echo './'`../src/misc/hash_aligner.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o options_description.o `test -f '../src/misc/options_description.cpp' || echo './'`../src/misc/options_description.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o log.o `test -f '../src/misc/log.cpp' || echo './'`../src/misc/log.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/misc/hash_aligner.h:14,
from ../src/misc/hash_aligner.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/functional:49,
from ../src/basic/functional.h:13,
from ../src/container/hash_map.h:13:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/misc/log.cpp: In destructor 'LogProcess::~LogProcess()':
../src/misc/log.cpp:78:13: warning: 'throw' will always call 'terminate' [-Wterminate]
78 | throw runtime_error("cannot kill log process");
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../src/misc/log.cpp:78:13: note: in C++11 destructors default to 'noexcept'
../src/misc/log.cpp: In static member function 'static void* LogThread::LogThreadFunc(void*)':
../src/misc/log.cpp:122:14: warning: ignoring return value of 'ssize_t write(int, const void*, size_t)' declared with attribute 'warn_unused_result' [-Wunused-result]
122 | write(log_thread.out_fd, line, len);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o utils.o `test -f '../src/misc/utils.cpp' || echo './'`../src/misc/utils.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/algorithm:61,
from ../src/basic/math.cpp:3:
/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,
| ^~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from ../src/basic/math.h:13,
from ../src/basic/math.cpp:1:
/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>::
| ^~~~~~~~~~~~~~~~~~~
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 GenerateNormalCDFTable(int, int, std::vector<double>&)' at ../src/basic/math.cpp:40:31:
/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 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 'void GenerateNormalCDFTable(int, int, std::vector<double>&)' at ../src/basic/math.cpp:41:9:
/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);
| ~~~~~~~
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]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
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 'void GenerateNormalCDFTable(int, int, std::vector<double>&)' at ../src/basic/math.cpp:41:9:
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o blat_record.o `test -f '../src/misc/blat_record.cpp' || echo './'`../src/misc/blat_record.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o short_sequence.o `test -f '../src/sequence/short_sequence.cpp' || echo './'`../src/sequence/short_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_reader.o `test -f '../src/sequence/sequence_reader.cpp' || echo './'`../src/sequence/sequence_reader.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_writer.o `test -f '../src/sequence/sequence_writer.cpp' || echo './'`../src/sequence/sequence_writer.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_io.o `test -f '../src/sequence/sequence_io.cpp' || echo './'`../src/sequence/sequence_io.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence.o `test -f '../src/sequence/sequence.cpp' || echo './'`../src/sequence/sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o compact_sequence.o `test -f '../src/sequence/compact_sequence.cpp' || echo './'`../src/sequence/compact_sequence.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph_branch_group.o `test -f '../src/graph/contig_graph_branch_group.cpp' || echo './'`../src/graph/contig_graph_branch_group.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph.o `test -f '../src/graph/hash_graph.cpp' || echo './'`../src/graph/hash_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold_graph.o `test -f '../src/graph/scaffold_graph.cpp' || echo './'`../src/graph/scaffold_graph.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/graph/contig_graph_branch_group.h:15,
from ../src/graph/contig_graph_branch_group.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from ../src/graph/contig_graph_branch_group.h:13:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/graph/hash_graph.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/graph/hash_graph.h:15:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/graph/scaffold_graph.h:19,
from ../src/graph/scaffold_graph.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/graph/scaffold_graph.h:14:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_graph.o `test -f '../src/graph/contig_graph.cpp' || echo './'`../src/graph/contig_graph.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/graph/contig_graph.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/graph/contig_graph.h:14:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_graph_branch_group.o `test -f '../src/graph/hash_graph_branch_group.cpp' || echo './'`../src/graph/hash_graph_branch_group.cpp
../src/graph/contig_graph.cpp: In member function 'void ContigGraph::TopSort(std::deque<ContigGraphVertexAdaptor>&, std::deque<ContigGraphVertexAdaptor>&)':
../src/graph/contig_graph.cpp:1391:30: warning: variable 'end' set but not used [-Wunused-but-set-variable]
1391 | ContigGraphVertexAdaptor end = GetEndVertexAdaptor(component);
| ^~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/graph/hash_graph_branch_group.h:14,
from ../src/graph/hash_graph_branch_group.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/graph/hash_graph.h:15:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o contig_info.o `test -f '../src/graph/contig_info.cpp' || echo './'`../src/graph/contig_info.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o local_assembler.o `test -f '../src/assembly/local_assembler.cpp' || echo './'`../src/assembly/local_assembler.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o assembly_utility.o `test -f '../src/assembly/assembly_utility.cpp' || echo './'`../src/assembly/assembly_utility.cpp
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/assembly/local_assembler.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/assembly/assembly_utility.h:17,
from ../src/assembly/local_assembler.h:13:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/assembly/assembly_utility.cpp:14:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/assembly/assembly_utility.h:17,
from ../src/assembly/assembly_utility.cpp:9:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/assembly/local_assembler.cpp: In static member function 'static void* LocalAssemblerWithReference::LocalAssembleThread(void*)':
../src/assembly/local_assembler.cpp:488:22: warning: variable 'flag' set but not used [-Wunused-but-set-variable]
488 | bool flag = false;
| ^~~~
../src/assembly/local_assembler.cpp:489:21: warning: variable 'aligned' set but not used [-Wunused-but-set-variable]
489 | int aligned[2] = {0};
| ^~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest-all.o `test -f '../gtest_src/gtest/gtest-all.cc' || echo './'`../gtest_src/gtest/gtest-all.cc
In file included from ../gtest_src/gtest/gtest-all.cc:39:
../gtest_src/gtest/gtest.h: In static member function 'static const char* testing::internal::String::CloneCString(const char*)':
../gtest_src/gtest/gtest.h:2672:17: warning: 'char* __builtin_strncpy(char*, const char*, unsigned int)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
2672 | return strncpy(dest, src, n);
| ^
../gtest_src/gtest/gtest-all.cc:2155:39: note: length computed here
2155 | NULL : CloneString(c_str, strlen(c_str));
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
rm -f libassembly.a
ar cru libassembly.a math.o hash_aligner.o options_description.o log.o utils.o blat_record.o short_sequence.o sequence_reader.o sequence_writer.o sequence_io.o sequence.o compact_sequence.o contig_graph_branch_group.o hash_graph.o scaffold_graph.o contig_graph.o hash_graph_branch_group.o contig_info.o local_assembler.o assembly_utility.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libassembly.a
rm -f libgtest.a
ar cru libgtest.a gtest_main.o gtest-all.o
ar: `u' modifier ignored since `D' is the default (see `U')
ranlib libgtest.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib'
Making all in bin
make[3]: Entering directory '/<<PKGBUILDDIR>>/bin'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba.o `test -f '../src/release/idba.cpp' || echo './'`../src/release/idba.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_ud.o `test -f '../src/release/idba_ud.cpp' || echo './'`../src/release/idba_ud.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran.o `test -f '../src/release/idba_tran.cpp' || echo './'`../src/release/idba_tran.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_hybrid.o `test -f '../src/release/idba_hybrid.cpp' || echo './'`../src/release/idba_hybrid.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/release/idba.cpp:23:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/release/idba.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/release/idba_tran.cpp:22:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/release/idba_tran.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/release/idba_ud.cpp:21:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/release/idba_ud.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/release/idba_hybrid.cpp:21:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/release/idba_hybrid.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/release/idba_tran.cpp: In function 'void FindIsoforms(ContigGraphPath&, std::deque<ContigGraphPath>&, ContigGraph&, std::deque<ContigGraphPath>&)':
../src/release/idba_tran.cpp:241:33: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
241 | if (flag && path.size() > option.min_transcript)
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/release/idba_tran.cpp: In function 'void Assemble(HashGraph&)':
../src/release/idba_tran.cpp:523:35: warning: comparison of integer expressions of different signedness: 'uint32_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
523 | if (transcripts[i].size() >= option.min_transcript)
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o shuffle_reads.o `test -f '../src/tools/shuffle_reads.cpp' || echo './'`../src/tools/shuffle_reads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o scaffold.o `test -f '../src/tools/scaffold.cpp' || echo './'`../src/tools/scaffold.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_component.o `test -f '../src/tools/validate_component.cpp' || echo './'`../src/tools/validate_component.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fa2fq.o `test -f '../src/tools/fa2fq.cpp' || echo './'`../src/tools/fa2fq.cpp
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/tools/scaffold.cpp:21:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/tools/scaffold.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/tools/validate_component.cpp: In function 'int main(int, char**)':
../src/tools/validate_component.cpp:141:13: warning: unused variable 'ref_id' [-Wunused-variable]
141 | int ref_id = dict[record.ref_name];
| ^~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_rna.o `test -f '../src/tools/validate_rna.cpp' || echo './'`../src/tools/validate_rna.cpp
../src/tools/validate_rna.cpp: In function 'int main(int, char**)':
../src/tools/validate_rna.cpp:396:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
396 | fscanf(flist, "%s %lf", buf, &coverage[i]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_mummer.o `test -f '../src/tools/validate_contigs_mummer.cpp' || echo './'`../src/tools/validate_contigs_mummer.cpp
../src/tools/validate_contigs_mummer.cpp: In function 'int main(int, char**)':
../src/tools/validate_contigs_mummer.cpp:218:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
218 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:219:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
219 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:220:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
220 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:221:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
221 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
../src/tools/validate_contigs_mummer.cpp:222:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
222 | fgets(line, MaxLine, fcoord);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o print_graph.o `test -f '../src/tools/print_graph.cpp' || echo './'`../src/tools/print_graph.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o idba_tran_test.o `test -f '../src/tools/idba_tran_test.cpp' || echo './'`../src/tools/idba_tran_test.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/tools/print_graph.cpp:9:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/graph/contig_graph.h:14:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from ../src/container/hash_table.h:23,
from ../src/graph/hash_graph.h:22,
from ../src/assembly/local_assembler.h:15,
from ../src/tools/idba_tran_test.cpp:21:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/deque:65,
from ../src/tools/idba_tran_test.cpp:11:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sample_reads.o `test -f '../src/tools/sample_reads.cpp' || echo './'`../src/tools/sample_reads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_psl.o `test -f '../src/tools/sort_psl.cpp' || echo './'`../src/tools/sort_psl.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sort_reads.o `test -f '../src/tools/sort_reads.cpp' || echo './'`../src/tools/sort_reads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_contigs.o `test -f '../src/tools/filter_contigs.cpp' || echo './'`../src/tools/filter_contigs.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_rna_blat.o `test -f '../src/tools/parallel_rna_blat.cpp' || echo './'`../src/tools/parallel_rna_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filter_blat.o `test -f '../src/tools/filter_blat.cpp' || echo './'`../src/tools/filter_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fa.o `test -f '../src/tools/split_fa.cpp' || echo './'`../src/tools/split_fa.cpp
../src/tools/parallel_rna_blat.cpp: In function 'void CreateFile(const std::string&)':
../src/tools/parallel_rna_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
47 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void RemoveFile(const std::string&)':
../src/tools/parallel_rna_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
53 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void Append(const std::string&, const std::string&)':
../src/tools/parallel_rna_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
59 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/tools/parallel_rna_blat.cpp: In function 'void RunBlat(const std::string&)':
../src/tools/parallel_rna_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
96 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o test.o `test -f '../src/tools/test.cpp' || echo './'`../src/tools/test.cpp
../src/tools/test.cpp:6:32: warning: extra tokens at end of #include directive
6 | #include "graph/contig_graph.h";
| ^
../src/tools/test.cpp:7:31: warning: extra tokens at end of #include directive
7 | #include "sequence/sequence.h";
| ^
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_reads_blat.o `test -f '../src/tools/validate_reads_blat.cpp' || echo './'`../src/tools/validate_reads_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_fq.o `test -f '../src/tools/split_fq.cpp' || echo './'`../src/tools/split_fq.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/graph/contig_graph.h:19,
from ../src/tools/test.cpp:6:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/ostream:38,
from /usr/include/c++/12/iostream:39,
from ../src/tools/test.cpp:1:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o fq2fa.o `test -f '../src/release/fq2fa.cpp' || echo './'`../src/release/fq2fa.cpp
In file included from /usr/include/c++/12/vector:70,
from ../src/tools/validate_reads_blat.cpp:16:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:523:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
523 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o validate_contigs_blat.o `test -f '../src/release/validate_contigs_blat.cpp' || echo './'`../src/release/validate_contigs_blat.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at ../src/tools/validate_reads_blat.cpp:71:24:
/usr/include/c++/12/bits/stl_vector.h:1032:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1032 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o raw_n50.o `test -f '../src/release/raw_n50.cpp' || echo './'`../src/release/raw_n50.cpp
../src/release/validate_contigs_blat.cpp: In function 'int main(int, char**)':
../src/release/validate_contigs_blat.cpp:388:19: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
388 | fscanf(flist, "%s %lf", buf, &coverage[i]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o parallel_blat.o `test -f '../src/release/parallel_blat.cpp' || echo './'`../src/release/parallel_blat.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sim_reads_tran.o `test -f '../src/release/sim_reads_tran.cpp' || echo './'`../src/release/sim_reads_tran.cpp
../src/release/parallel_blat.cpp: In function 'void CreateFile(const std::string&)':
../src/release/parallel_blat.cpp:47:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
47 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void RemoveFile(const std::string&)':
../src/release/parallel_blat.cpp:53:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
53 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void Append(const std::string&, const std::string&)':
../src/release/parallel_blat.cpp:59:11: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
59 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/release/parallel_blat.cpp: In function 'void RunBlat(const std::string&)':
../src/release/parallel_blat.cpp:96:19: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
96 | system(cmd.c_str());
| ~~~~~~^~~~~~~~~~~~~
../src/release/sim_reads_tran.cpp: In function 'int main(int, char**)':
../src/release/sim_reads_tran.cpp:89:15: warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)' declared with attribute 'warn_unused_result' [-Wunused-result]
89 | fscanf(flist, "%s %lf", buf, &weight[i]);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o filterfa.o `test -f '../src/release/filterfa.cpp' || echo './'`../src/release/filterfa.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o split_scaffold.o `test -f '../src/release/split_scaffold.cpp' || echo './'`../src/release/split_scaffold.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../gtest_src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sim_reads.o `test -f '../src/release/sim_reads.cpp' || echo './'`../src/release/sim_reads.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba idba.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_ud idba_ud.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran idba_tran.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_hybrid idba_hybrid.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o shuffle_reads shuffle_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o scaffold scaffold.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_component validate_component.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fa2fq fa2fq.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_rna validate_rna.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_mummer validate_contigs_mummer.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o print_graph print_graph.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o idba_tran_test idba_tran_test.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sample_reads sample_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_psl sort_psl.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sort_reads sort_reads.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_contigs filter_contigs.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_rna_blat parallel_rna_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filter_blat filter_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fa split_fa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o test test.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_reads_blat validate_reads_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_fq split_fq.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o fq2fa fq2fa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o validate_contigs_blat validate_contigs_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o raw_n50 raw_n50.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o parallel_blat parallel_blat.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads_tran sim_reads_tran.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o filterfa filterfa.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o split_scaffold split_scaffold.o ../lib/libassembly.a -latomic
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sim_reads sim_reads.o ../lib/libassembly.a -latomic
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making all in test
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making all in script
make[3]: Entering directory '/<<PKGBUILDDIR>>/script'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/script'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<PKGBUILDDIR>>'
# /usr/bin/make unittest
export PATH=/<<PKGBUILDDIR>>/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games && cd test && /usr/bin/make check
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
/usr/bin/make compact_sequence_unittest hash_table_unittest bit_edges_unittest kmer_unittest hash_set_unittest atomic_integer_unittest vertex_status_unittest histgram_unittest managed_list_unittest sequence_unittest short_sequence_unittest hash_map_unittest
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o gtest_main.o `test -f '../gtest_src/gtest/gtest_main.cc' || echo './'`../gtest_src/gtest/gtest_main.cc
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o compact_sequence_unittest.o `test -f '../src/test/compact_sequence_unittest.cpp' || echo './'`../src/test/compact_sequence_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o compact_sequence_unittest gtest_main.o compact_sequence_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_table_unittest.o `test -f '../src/test/hash_table_unittest.cpp' || echo './'`../src/test/hash_table_unittest.cpp
In file included from ../src/container/hash_table.h:23,
from ../src/test/hash_table_unittest.cpp:11:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/unique_ptr.h:37,
from /usr/include/c++/12/memory:76,
from /usr/include/gtest/gtest.h:54,
from ../src/test/hash_table_unittest.cpp:9:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from /usr/include/gtest/internal/gtest-internal.h:62,
from /usr/include/gtest/gtest-printers.h:114,
from /usr/include/gtest/gtest-matchers.h:48,
from /usr/include/gtest/internal/gtest-death-test-internal.h:46,
from /usr/include/gtest/gtest-death-test.h:43,
from /usr/include/gtest/gtest.h:60:
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = Kmer; _Val = std::pair<const Kmer, int>; _KeyOfValue = std::_Select1st<std::pair<const Kmer, int> >; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]':
/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const Kmer&>, std::tuple<>}; _Key = Kmer; _Val = std::pair<const Kmer, int>; _KeyOfValue = std::_Select1st<std::pair<const Kmer, int> >; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Kmer; _Tp = int; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]',
inlined from 'virtual void HashTableTest_Iterator_Test::TestBody()' at ../src/test/hash_table_unittest.cpp:111:9:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Kmer; _Tp = int; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]',
inlined from 'virtual void HashTableTest_Find_Test::TestBody()' at ../src/test/hash_table_unittest.cpp:145:9:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Kmer; _Tp = int; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]',
inlined from 'virtual void HashTableTest_WriteAndRead_Test::TestBody()' at ../src/test/hash_table_unittest.cpp:228:9:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Kmer; _Tp = int; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]',
inlined from 'virtual void HashTableTest::SetUp()' at ../src/test/hash_table_unittest.cpp:72:30:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_table_unittest gtest_main.o hash_table_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o bit_edges_unittest.o `test -f '../src/test/bit_edges_unittest.cpp' || echo './'`../src/test/bit_edges_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o bit_edges_unittest gtest_main.o bit_edges_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o kmer_unittest.o `test -f '../src/test/kmer_unittest.cpp' || echo './'`../src/test/kmer_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o kmer_unittest gtest_main.o kmer_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_set_unittest.o `test -f '../src/test/hash_set_unittest.cpp' || echo './'`../src/test/hash_set_unittest.cpp
In file included from ../src/container/hash_set.h:13,
from ../src/test/hash_set_unittest.cpp:12:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/unique_ptr.h:37,
from /usr/include/c++/12/memory:76,
from /usr/include/gtest/gtest.h:54,
from ../src/test/hash_set_unittest.cpp:10:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_set_unittest gtest_main.o hash_set_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o atomic_integer_unittest.o `test -f '../src/test/atomic_integer_unittest.cpp' || echo './'`../src/test/atomic_integer_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o atomic_integer_unittest gtest_main.o atomic_integer_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o vertex_status_unittest.o `test -f '../src/test/vertex_status_unittest.cpp' || echo './'`../src/test/vertex_status_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o vertex_status_unittest gtest_main.o vertex_status_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o histgram_unittest.o `test -f '../src/test/histgram_unittest.cpp' || echo './'`../src/test/histgram_unittest.cpp
In file included from /usr/include/c++/12/bits/stl_algo.h:60,
from /usr/include/c++/12/functional:64,
from /usr/include/gtest/gtest-printers.h:104,
from /usr/include/gtest/gtest-matchers.h:48,
from /usr/include/gtest/internal/gtest-death-test-internal.h:46,
from /usr/include/gtest/gtest-death-test.h:43,
from /usr/include/gtest/gtest.h:60,
from ../src/test/histgram_unittest.cpp:9:
/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,
| ^~~~~~~~~~~~~
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /usr/include/gtest/gtest.h:57:
/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>::
| ^~~~~~~~~~~~~~~~~~~
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 'virtual void HistgramTest::SetUp()' at ../src/test/histgram_unittest.cpp:26:24:
/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 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 HistgramTest_Median_Test::TestBody()' at ../src/test/histgram_unittest.cpp:132:9:
/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);
| ~~~~~~~
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]',
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /usr/include/c++/12/bits/stl_algo.h:1940:31,
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 HistgramTest_Median_Test::TestBody()' at ../src/test/histgram_unittest.cpp:132:9:
/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);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o histgram_unittest gtest_main.o histgram_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o managed_list_unittest.o `test -f '../src/test/managed_list_unittest.cpp' || echo './'`../src/test/managed_list_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o managed_list_unittest gtest_main.o managed_list_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o sequence_unittest.o `test -f '../src/test/sequence_unittest.cpp' || echo './'`../src/test/sequence_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o sequence_unittest gtest_main.o sequence_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o short_sequence_unittest.o `test -f '../src/test/short_sequence_unittest.cpp' || echo './'`../src/test/short_sequence_unittest.cpp
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o short_sequence_unittest gtest_main.o short_sequence_unittest.o ../lib/libassembly.a -lgtest -latomic
g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -c -o hash_map_unittest.o `test -f '../src/test/hash_map_unittest.cpp' || echo './'`../src/test/hash_map_unittest.cpp
In file included from ../src/container/hash_map.h:14,
from ../src/test/hash_map_unittest.cpp:11:
../src/basic/hash.h:18:26: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
18 | struct Hash: public std::unary_function<T, uint64_t>
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/unique_ptr.h:37,
from /usr/include/c++/12/memory:76,
from /usr/include/gtest/gtest.h:54,
from ../src/test/hash_map_unittest.cpp:9:
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:25:34: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
25 | struct Hash<int8_t>: public std::unary_function<int8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:32:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
32 | struct Hash<uint8_t>: public std::unary_function<uint8_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:39:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
39 | struct Hash<int16_t>: public std::unary_function<int16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:46:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
46 | struct Hash<uint16_t>: public std::unary_function<uint16_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:53:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
53 | struct Hash<int32_t>: public std::unary_function<int32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:60:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
60 | struct Hash<uint32_t>: public std::unary_function<uint32_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:67:35: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
67 | struct Hash<int64_t>: public std::unary_function<int64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
../src/basic/hash.h:74:36: warning: 'template<class _Arg, class _Result> struct std::unary_function' is deprecated [-Wdeprecated-declarations]
74 | struct Hash<uint64_t>: public std::unary_function<uint64_t, uint64_t>
| ^~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:117:12: note: declared here
117 | struct unary_function
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from /usr/include/gtest/internal/gtest-internal.h:62,
from /usr/include/gtest/gtest-printers.h:114,
from /usr/include/gtest/gtest-matchers.h:48,
from /usr/include/gtest/internal/gtest-death-test-internal.h:46,
from /usr/include/gtest/gtest-death-test.h:43,
from /usr/include/gtest/gtest.h:60:
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = Kmer; _Val = std::pair<const Kmer, int>; _KeyOfValue = std::_Select1st<std::pair<const Kmer, int> >; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]':
/usr/include/c++/12/bits/stl_tree.h:2209:5: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
2209 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const Kmer&>, std::tuple<>}; _Key = Kmer; _Val = std::pair<const Kmer, int>; _KeyOfValue = std::_Select1st<std::pair<const Kmer, int> >; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Kmer; _Tp = int; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]',
inlined from 'virtual void HashMapTest_Iterator_Test::TestBody()' at ../src/test/hash_map_unittest.cpp:72:9:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Kmer; _Tp = int; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]',
inlined from 'virtual void HashMapTest::SetUp()' at ../src/test/hash_map_unittest.cpp:34:28:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = Kmer; _Tp = int; _Compare = std::less<Kmer>; _Alloc = std::allocator<std::pair<const Kmer, int> >]',
inlined from 'virtual void HashMapTest_Find_Test::TestBody()' at ../src/test/hash_map_unittest.cpp:108:9:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<Kmer, std::pair<const Kmer, int>, std::_Select1st<std::pair<const Kmer, int> >, std::less<Kmer>, std::allocator<std::pair<const Kmer, int> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
g++ -Wall -O3 -fopenmp -pthread -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -fopenmp -pthread -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -o hash_map_unittest gtest_main.o hash_map_unittest.o ../lib/libassembly.a -lgtest -latomic
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
/usr/bin/make check-TESTS
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[4]: Entering directory '/<<PKGBUILDDIR>>/test'
PASS: compact_sequence_unittest
PASS: hash_table_unittest
PASS: bit_edges_unittest
PASS: kmer_unittest
PASS: hash_set_unittest
PASS: atomic_integer_unittest
PASS: vertex_status_unittest
PASS: histgram_unittest
PASS: managed_list_unittest
PASS: sequence_unittest
PASS: short_sequence_unittest
PASS: hash_map_unittest
============================================================================
Testsuite summary for idba 1.1.3
============================================================================
# TOTAL: 12
# PASS: 12
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[4]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
create-stamp debian/debhelper-build-stamp
dh_prep -a
dh_installdirs -a
dh_auto_install -a
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/tmp AM_UPDATE_INFO_DIR=no
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Making install in lib
make[2]: Entering directory '/<<PKGBUILDDIR>>/lib'
make[3]: Entering directory '/<<PKGBUILDDIR>>/lib'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/lib'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/lib'
Making install in bin
make[2]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[3]: Entering directory '/<<PKGBUILDDIR>>/bin'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c idba idba_ud idba_tran idba_hybrid '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/bin'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/bin'
Making install in test
make[2]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Entering directory '/<<PKGBUILDDIR>>/test'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/test'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/test'
Making install in script
make[2]: Entering directory '/<<PKGBUILDDIR>>/script'
make[3]: Entering directory '/<<PKGBUILDDIR>>/script'
make[3]: Nothing to be done for 'install-data-am'.
/bin/mkdir -p '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
/usr/bin/install -c scan.py run-unittest.py validate_blat validate_blat_parallel '/<<PKGBUILDDIR>>/debian/tmp/usr/bin'
make[3]: Leaving directory '/<<PKGBUILDDIR>>/script'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/script'
make[2]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Entering directory '/<<PKGBUILDDIR>>'
make[3]: Nothing to be done for 'install-exec-am'.
make[3]: Nothing to be done for 'install-data-am'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>'
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
# for the moment the role of these scripts is totally unknown but they do not seem to be necessary
mv debian/idba/usr/bin/*.py debian/idba/usr/lib/idba/
mv debian/idba/usr/bin/validate_blat* debian/idba/usr/lib/idba/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/parallel_rna_blat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/filter_contigs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/filter_blat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/raw_n50 contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_hybrid contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_tran contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sim_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/print_graph contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/validate_reads_blat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba/usr/bin/idba_ud contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/split_fa 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/idba/usr/bin/idba_hybrid debian/idba/usr/bin/idba_tran debian/idba/usr/bin/idba debian/idba/usr/bin/idba_ud were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/split_scaffold contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/parallel_blat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/split_fq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/validate_rna contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sort_psl contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/fa2fq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sample_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/scaffold contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/validate_component contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sort_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/fq2fa contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/sim_reads_tran contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/validate_contigs_mummer contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/shuffle_reads contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/idba-extra/usr/bin/validate_contigs_blat 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/idba-extra/usr/bin/parallel_rna_blat debian/idba-extra/usr/bin/filter_contigs debian/idba-extra/usr/bin/filter_blat debian/idba-extra/usr/bin/raw_n50 debian/idba-extra/usr/bin/sim_reads debian/idba-extra/usr/bin/print_graph debian/idba-extra/usr/bin/validate_reads_blat debian/idba-extra/usr/bin/split_fa debian/idba-extra/usr/bin/split_scaffold debian/idba-extra/usr/bin/parallel_blat debian/idba-extra/usr/bin/split_fq debian/idba-extra/usr/bin/validate_rna debian/idba-extra/usr/bin/sort_psl debian/idba-extra/usr/bin/fa2fq debian/idba-extra/usr/bin/sample_reads debian/idba-extra/usr/bin/scaffold debian/idba-extra/usr/bin/validate_component debian/idba-extra/usr/bin/sort_reads debian/idba-extra/usr/bin/fq2fa debian/idba-extra/usr/bin/sim_reads_tran debian/idba-extra/usr/bin/validate_contigs_mummer debian/idba-extra/usr/bin/shuffle_reads debian/idba-extra/usr/bin/validate_contigs_blat were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package idba: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'idba' in '../idba_1.1.3-8_armhf.deb'.
dpkg-deb: building package 'idba-dbgsym' in '../idba-dbgsym_1.1.3-8_armhf.deb'.
dpkg-deb: building package 'idba-extra' in '../idba-extra_1.1.3-8_armhf.deb'.
dpkg-deb: building package 'idba-extra-dbgsym' in '../idba-extra-dbgsym_1.1.3-8_armhf.deb'.
dpkg-genbuildinfo --build=any -O../idba_1.1.3-8_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../idba_1.1.3-8_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 2022-11-08T08:02:09Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
idba_1.1.3-8_armhf.changes:
---------------------------
Format: 1.8
Date: Sat, 05 Nov 2022 21:27:52 +0100
Source: idba
Binary: idba idba-dbgsym idba-extra idba-extra-dbgsym
Architecture: armhf
Version: 1.1.3-8
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
idba - iterative De Bruijn Graph short read assemblers
idba-extra - iterative De Bruijn Graph short read assemblers (extra tools)
Changes:
idba (1.1.3-8) unstable; urgency=medium
.
* Fix watch file
* Standards-Version: 4.6.1 (routine-update)
* debhelper-compat 13 (routine-update)
* Fix dh_missingwq
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
idba-dbgsym_1.1.3-8_armhf.deb
-----------------------------
new Debian package, version 2.0.
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483 bytes, 12 lines control
508 bytes, 5 lines md5sums
Package: idba-dbgsym
Source: idba
Version: 1.1.3-8
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Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10139
Depends: idba (= 1.1.3-8)
Section: debug
Priority: optional
Description: debug symbols for idba
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lrwxrwxrwx root/root 0 2022-11-05 20:27 ./usr/share/doc/idba-dbgsym -> idba
idba-extra-dbgsym_1.1.3-8_armhf.deb
-----------------------------------
new Debian package, version 2.0.
size 7955548 bytes: control archive=1652 bytes.
1279 bytes, 12 lines control
2528 bytes, 24 lines md5sums
Package: idba-extra-dbgsym
Source: idba
Version: 1.1.3-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 8584
Depends: idba-extra (= 1.1.3-8)
Section: debug
Priority: optional
Description: debug symbols for idba-extra
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lrwxrwxrwx root/root 0 2022-11-05 20:27 ./usr/share/doc/idba-extra-dbgsym -> idba-extra
idba-extra_1.1.3-8_armhf.deb
----------------------------
new Debian package, version 2.0.
size 304096 bytes: control archive=1888 bytes.
1472 bytes, 30 lines control
1765 bytes, 30 lines md5sums
Package: idba-extra
Source: idba
Version: 1.1.3-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2471
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 11), python3, idba
Section: science
Priority: optional
Homepage: https://github.com/loneknightpy/idba
Description: iterative De Bruijn Graph short read assemblers (extra tools)
IDBA stands for iterative de Bruijn graph assembler. In computational
sequence biology, an assembler solves the puzzle coming from large
sequencing machines that feature many gigabytes of short reads from a
large genome.
.
This package provides several flavours of the IDBA assembler, as they all
share the same source tree but serve different purposes and evolved over time.
.
IDBA is the basic iterative de Bruijn graph assembler for
second-generation sequencing reads. IDBA-UD, an extension of IDBA,
is designed to utilize paired-end reads to assemble low-depth regions
and use progressive depth on contigs to reduce errors in high-depth
regions. It is a generic purpose assembler and especially good for
single-cell and metagenomic sequencing data. IDBA-Hybrid is another
update version of IDBA-UD, which can make use of a similar reference
genome to improve assembly result. IDBA-Tran is an iterative de Bruijn
graph assembler for RNA-Seq data.
.
This package ships extra tools for using idba in specific situations.
drwxr-xr-x root/root 0 2022-11-05 20:27 ./
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-rw-r--r-- root/root 2585 2022-11-05 20:27 ./usr/share/doc/idba-extra/copyright
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-rw-r--r-- root/root 460 2022-11-05 20:27 ./usr/share/man/man1/sim_reads_tran.1.gz
idba_1.1.3-8_armhf.deb
----------------------
new Debian package, version 2.0.
size 559064 bytes: control archive=1692 bytes.
1359 bytes, 27 lines control
1599 bytes, 23 lines md5sums
Package: idba
Version: 1.1.3-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3601
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libgomp1 (>= 6), libstdc++6 (>= 11), python3
Section: science
Priority: optional
Homepage: https://github.com/loneknightpy/idba
Description: iterative De Bruijn Graph short read assemblers
IDBA stands for iterative de Bruijn graph assembler. In computational
sequence biology, an assembler solves the puzzle coming from large
sequencing machines that feature many gigabytes of short reads from a
large genome.
.
This package provides several flavours of the IDBA assembler, as they all
share the same source tree but serve different purposes and evolved over time.
.
IDBA is the basic iterative de Bruijn graph assembler for
second-generation sequencing reads. IDBA-UD, an extension of IDBA,
is designed to utilize paired-end reads to assemble low-depth regions
and use progressive depth on contigs to reduce errors in high-depth
regions. It is a generic purpose assembler and especially good for
single-cell and metagenomic sequencing data. IDBA-Hybrid is another
update version of IDBA-UD, which can make use of a similar reference
genome to improve assembly result. IDBA-Tran is an iterative de Bruijn
graph assembler for RNA-Seq data.
drwxr-xr-x root/root 0 2022-11-05 20:27 ./
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-rw-r--r-- root/root 565135 2022-11-05 20:27 ./usr/share/doc/idba/examples/tran/found-transcripts.fa
-rw-r--r-- root/root 886740 2022-11-05 20:27 ./usr/share/doc/idba/examples/tran/found-transcripts.fa.list
drwxr-xr-x root/root 0 2022-11-05 20:27 ./usr/share/doc/idba/examples/ud/
-rw-r--r-- root/root 5072 2022-11-05 20:27 ./usr/share/doc/idba/examples/ud/220668.fa
-rw-r--r-- root/root 5098 2022-11-05 20:27 ./usr/share/doc/idba/examples/ud/321956.fa
-rw-r--r-- root/root 5084 2022-11-05 20:27 ./usr/share/doc/idba/examples/ud/557433.fa
drwxr-xr-x root/root 0 2022-11-05 20:27 ./usr/share/man/
drwxr-xr-x root/root 0 2022-11-05 20:27 ./usr/share/man/man1/
-rw-r--r-- root/root 813 2022-11-05 20:27 ./usr/share/man/man1/idba.1.gz
-rw-r--r-- root/root 941 2022-11-05 20:27 ./usr/share/man/man1/idba_hybrid.1.gz
-rw-r--r-- root/root 856 2022-11-05 20:27 ./usr/share/man/man1/idba_tran.1.gz
-rw-r--r-- root/root 905 2022-11-05 20:27 ./usr/share/man/man1/idba_ud.1.gz
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 283344
Build-Time: 1381
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 484
Job: idba_1.1.3-8
Machine Architecture: armhf
Package: idba
Package-Time: 1926
Source-Version: 1.1.3-8
Space: 283344
Status: successful
Version: 1.1.3-8
--------------------------------------------------------------------------------
Finished at 2022-11-08T08:02:09Z
Build needed 00:32:06, 283344k disc space