ivar →
1.4.2+dfsg-3 →
armhf → 2024-02-21 19:49:31
sbuild (Debian sbuild) 0.85.0 (04 January 2023) on test2023
+==============================================================================+
| ivar 1.4.2+dfsg-3 (armhf) Wed, 21 Feb 2024 19:47:40 +0000 |
+==============================================================================+
Package: ivar
Version: 1.4.2+dfsg-3
Source Version: 1.4.2+dfsg-3
Distribution: trixie-staging
Machine Architecture: arm64
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-6c54412f-a7ef-4df0-8875-0006f414271f' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/ivar-Kd9KcB/resolver-9vf5qE' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.5 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.1 MB]
Fetched 29.6 MB in 5s (5553 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-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: 'ivar' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/ivar.git
Please use:
git clone https://salsa.debian.org/med-team/ivar.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 721 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main ivar 1.4.2+dfsg-3 (dsc) [2205 B]
Get:2 http://172.17.4.1/private trixie-staging/main ivar 1.4.2+dfsg-3 (tar) [673 kB]
Get:3 http://172.17.4.1/private trixie-staging/main ivar 1.4.2+dfsg-3 (diff) [46.3 kB]
Fetched 721 kB in 0s (4334 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/ivar-Kd9KcB/ivar-1.4.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ivar-Kd9KcB' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libhts-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), libhts-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [629 B]
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Reading package lists...
Reading package lists...
Install main build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
librtmp1 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config
liblzma-doc libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl publicsuffix
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
librtmp1 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded.
Need to get 22.9 MB of archives.
After this operation, 82.4 MB of additional disk space will be used.
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Get:2 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf sensible-utils all 0.0.22 [22.4 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
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Get:10 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
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Get:14 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.13 [85.0 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:24 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.13 [889 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.59.0-1 [61.9 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-4 [195 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.5.0-2+rpi1 [372 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 8.5.0-2+rpi1 [456 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.19-1 [39.0 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.19-1 [46.7 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.6.0-1 [60.3 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.19+ds-1 [385 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.5-0.3 [278 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.3.dfsg-3 [903 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libhts-dev armhf 1.19+ds-1 [1560 kB]
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 6.1.47-v8+ #1 SMP PREEMPT Fri Sep 1 07:05:33 BST 2023 arm64 (aarch64)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.4+rpi1 g++-12_12.3.0-14+rpi1 g++-13_13.2.0-9+rpi1 gcc-12_12.3.0-14+rpi1 gcc-13_13.2.0-9+rpi1 libc6-dev_2.37-15~deb13u1+rpi1 libstdc++-12-dev_12.3.0-14+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 linux-libc-dev_6.5.6-1+rpi1+b1
Package versions: adduser_3.137 apt_2.7.11 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.4-3 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-14+rpi1 cpp-13_13.2.0-9+rpi1 dash_0.5.12-6 debconf_1.5.86 debhelper_13.13 debianutils_5.16 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.4+rpi1 dpkg-dev_1.22.4+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.33-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-14+rpi1 g++-13_13.2.0-9+rpi1 gcc_4:13.2.0-1+rpi1 gcc-10-base_10.4.0-7+rpi1 gcc-12_12.3.0-14+rpi1 gcc-12-base_12.3.0-14+rpi1 gcc-13_13.2.0-9+rpi1 gcc-13-base_13.2.0-9+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_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-4 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-1 libapt-pkg6.0_2.7.11 libarchive-zip-perl_1.68-1 libasan8_13.2.0-9+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-9+rpi1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2 libaudit1_1:3.1.2-2 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-6 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-15~deb13u1+rpi1 libc-dev-bin_2.37-15~deb13u1+rpi1 libc6_2.37-15~deb13u1+rpi1 libc6-dev_2.37-15~deb13u1+rpi1 libcap-ng0_0.8.4-2 libcap2_1:2.66-5 libcc1-0_13.2.0-9+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.5.0-2+rpi1 libcurl4-gnutls-dev_8.5.0-2+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.13 libdeflate-dev_1.19-1 libdeflate0_1.19-1 libdpkg-perl_1.22.4+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.33-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-14+rpi1 libgcc-13-dev_13.2.0-9+rpi1 libgcc-s1_13.2.0-9+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.3-1 libgomp1_13.2.0-9+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhts-dev_1.19+ds-1 libhts3_1.19+ds-1 libhtscodecs2_1.6.0-1 libicu72_72.1-4 libidn2-0_2.3.7-2 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-3 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1+b1 liblocale-gettext-perl_1.07-6+b1 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.5-0.3 liblzma5_5.4.5-0.3 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-2 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20240113-1 libnettle8_3.9.1-2 libnghttp2-14_1.59.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libperl5.38_5.38.2-3 libpipeline1_1.5.7-1 libpsl5_0.21.2-1+b1 libreadline8_8.2-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.5-1+rpi1 libselinux1_3.5-2 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-6 libsqlite3-0_3.45.1-1 libss2_1.47.0-2 libssh2-1_1.11.0-4 libssl3_3.1.5-1 libstdc++-12-dev_12.3.0-14+rpi1 libstdc++-13-dev_13.2.0-9+rpi1 libstdc++6_13.2.0-9+rpi1 libsub-override-perl_0.10-1 libsystemd0_255.3-1+rpi1 libtasn1-6_4.19.0-3 libtext-charwidth-perl_0.04-11+b1 libtext-glob-perl_0.11-3 libtext-iconv-perl_1.7-8+b1 libtinfo6_6.4+20240113-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-9+rpi1 libuchardet0_0.0.8-1 libudev1_255.3-1+rpi1 libunistring5_1.1-2 libuuid1_2.39.3-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1+b1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20240123-1 mount_2.39.3-6 nano_7.2-2 ncurses-base_6.4+20240113-1 ncurses-bin_6.4+20240113-1 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.38.2-3 perl-base_5.38.2-3 perl-modules-5.38_5.38.2-3 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.08-6 tar_1.35+dfsg-3 tzdata_2024a-1 usr-is-merged_39 usrmerge_39 util-linux_2.39.3-6 xz-utils_5.4.5-0.3 zlib1g_1:1.3.dfsg-3 zlib1g-dev_1:1.3.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: ivar
Binary: ivar, ivar-doc
Architecture: any all
Version: 1.4.2+dfsg-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>, Étienne Mollier <emollier@debian.org>
Homepage: https://github.com/andersen-lab/ivar
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/ivar
Vcs-Git: https://salsa.debian.org/med-team/ivar.git
Testsuite: autopkgtest
Testsuite-Triggers: samtools
Build-Depends: debhelper-compat (= 13), libhts-dev
Package-List:
ivar deb science optional arch=any
ivar-doc deb doc optional arch=all
Checksums-Sha1:
8424d860241b5fdb7cfbb71d8d8d85d6d9162962 672788 ivar_1.4.2+dfsg.orig.tar.xz
3c8e54454b0d7d0870d99a6a746dfc8c302980ce 46324 ivar_1.4.2+dfsg-3.debian.tar.xz
Checksums-Sha256:
87fbc667080e95823734eeca0dfcec058ff18f1aca7aff89de7a82217a7d2968 672788 ivar_1.4.2+dfsg.orig.tar.xz
ea91d32c705d08f6397c9234d3d127f7be201c2c176be4aa83e4f72b76363ab0 46324 ivar_1.4.2+dfsg-3.debian.tar.xz
Files:
d2c0875cd8d094e11207d0d185099282 672788 ivar_1.4.2+dfsg.orig.tar.xz
7b90003c4369da383c9942994b2e1f9c 46324 ivar_1.4.2+dfsg-3.debian.tar.xz
Dgit: cc92e3dc269b4f24682dfdaf04695cfc210a8aef debian archive/debian/1.4.2+dfsg-3 https://git.dgit.debian.org/ivar
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gpgv: Signature made Tue Dec 5 15:15:07 2023 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./ivar_1.4.2+dfsg-3.dsc: no acceptable signature found
dpkg-source: info: extracting ivar in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking ivar_1.4.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking ivar_1.4.2+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying Fix-warning.patch
dpkg-source: info: applying forward-build-options.patch
dpkg-source: info: applying privacy-breach.patch
dpkg-source: info: applying gcc-13.patch
dpkg-source: info: applying gcc-13-2.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=124
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-6c54412f-a7ef-4df0-8875-0006f414271f
SCHROOT_UID=114
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage --sanitize-env -us -uc -mRaspbian pi5 test autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package ivar
dpkg-buildpackage: info: source version 1.4.2+dfsg-3
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:12: installing './compile'
configure.ac:58: installing './config.guess'
configure.ac:58: installing './config.sub'
configure.ac:6: installing './install-sh'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/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 gawk... (cached) mawk
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 how to run the C preprocessor... gcc -E
checking for main in -lhts... no
checking for main in -lpthread... no
checking for main in -lz... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for unistd.h... (cached) yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for GNU libc compatible malloc... no
checking for GNU libc compatible realloc... no
checking for memmove... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<PKGBUILDDIR>>'
make all-recursive
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making all in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o ivar.o ivar.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o alignment.o alignment.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp
Using built-in specs.
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
Using built-in specs.
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plusCOLLECT_GCC=g++
-quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -WerrorCOLLECT_GCC=g++
-version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cchoZQ0G.sTarget: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
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Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
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Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
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GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
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GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
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GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
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Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
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Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
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Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
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GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
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GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
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End of search list.
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o call_consensus_pileup.o /tmp/ccqzbOH6.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'call_consensus_pileup.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc2wqzHT.s
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/13
/usr/include/arm-linux-gnueabihf/c++/13
/usr/include/c++/13/backward
/usr/lib/gcc/arm-linux-gnueabihf/13/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o suffix_tree.o /tmp/ccIn0nRE.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'suffix_tree.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccJtrBN8.s
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/13
/usr/include/arm-linux-gnueabihf/c++/13
/usr/include/c++/13/backward
/usr/lib/gcc/arm-linux-gnueabihf/13/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o trim_primer_quality.o /tmp/ccydYRsJ.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o remove_reads_from_amplicon.o /tmp/ccI95d9F.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'remove_reads_from_amplicon.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cczQYMCz.s
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'trim_primer_quality.'
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/13
/usr/include/arm-linux-gnueabihf/c++/13
/usr/include/c++/13/backward
/usr/lib/gcc/arm-linux-gnueabihf/13/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -dumpbase-ext .cpp -mfloat-abi=hardCompiler executable checksum: 623e3e7346050809c69d2706608bc9f7
-mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cctIH28Q.s
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
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End of search list.
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o call_variants.o /tmp/cc2wqzHT.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'call_variants.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccXYfRV8.s
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
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ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
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ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
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..
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End of search list.
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o get_masked_amplicons.o /tmp/cctIH28Q.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'get_masked_amplicons.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc6S7kAj.s
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
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..
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End of search list.
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o primer_bed.o /tmp/ccJtrBN8.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o allele_functions.o /tmp/cczQYMCz.s
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'primer_bed.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc9fic9B.s
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
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.
..
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/usr/lib/gcc/arm-linux-gnueabihf/13/include
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End of search list.
Compiler executable checksum: 623e3e7346050809c69d2706608bc9f7
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
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g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-9+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-9+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccPrRd2g.s
GNU C++17 (Raspbian 13.2.0-9+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
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ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
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End of search list.
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COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o interval_tree.o /tmp/ccPrRd2g.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
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LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'interval_tree.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o get_common_variants.o /tmp/ccXYfRV8.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
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LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'get_common_variants.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o ref_seq.o /tmp/cc9fic9B.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'ref_seq.'
In file included from /usr/include/c++/13/regex:59,
from parse_gff.h:6,
from parse_gff.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/13/regex:57:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’,
inlined from ‘std::vector<gff3_feature> gff3::query_features(uint64_t, std::string)’ at parse_gff.cpp:151:20:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘int gff3::read_file(std::string)’ at parse_gff.cpp:139:23:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
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Using built-in specs.
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make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making all in tests
make[3]: Entering directory '/<<PKGBUILDDIR>>/tests'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/tests'
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>>'
dh_auto_test --no-parallel
make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1
make[2]: Entering directory '/<<PKGBUILDDIR>>'
Making check in src
make[3]: Entering directory '/<<PKGBUILDDIR>>/src'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
Making check in tests
make[3]: Entering directory '/<<PKGBUILDDIR>>/tests'
make check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold
make[4]: Entering directory '/<<PKGBUILDDIR>>/tests'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_trim test_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_allele_depth test_allele_depth.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_seq_id test_consensus_seq_id.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_bed test_primer_bed.o ../src/primer_bed.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_getmasked.o test_getmasked.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_removereads.o test_removereads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_variants.o test_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/call_variants.o ../src/call_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp
In file included from /usr/include/c++/13/regex:59,
from ../src/parse_gff.h:6,
from ../src/parse_gff.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/13/regex:57:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’,
inlined from ‘std::vector<gff3_feature> gff3::query_features(uint64_t, std::string)’ at ../src/parse_gff.cpp:151:20:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘int gff3::read_file(std::string)’ at ../src/parse_gff.cpp:139:23:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_common_variants.o test_common_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_common_variants test_common_variants.o ../src/get_common_variants.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_isize_trim test_isize_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_interval_tree test_interval_tree.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_amplicon_search test_amplicon_search.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_min_insert_threshold.o test_consensus_min_insert_threshold.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_insert_threshold test_consensus_min_insert_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make check-TESTS
make[4]: Entering directory '/<<PKGBUILDDIR>>/tests'
make[5]: Entering directory '/<<PKGBUILDDIR>>/tests'
PASS: check_primer_trim
PASS: check_trim
PASS: check_quality_trim
PASS: check_consensus
PASS: check_allele_depth
PASS: check_consensus_threshold
PASS: check_consensus_min_depth
PASS: check_consensus_seq_id
PASS: check_primer_bed
PASS: check_getmasked
PASS: check_removereads
PASS: check_variants
PASS: check_common_variants
FAIL: check_unpaired_trim
PASS: check_primer_trim_edge_cases
PASS: check_isize_trim
PASS: check_interval_tree
PASS: check_amplicon_search
PASS: check_consensus_min_insert_threshold
======================================
ivar 1.4.2: tests/test-suite.log
======================================
# TOTAL: 19
# PASS: 18
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
.. contents:: :depth: 2
FAIL: check_unpaired_trim
=========================
Found 8 primers in BED file
test_72_280_12:1:0_11:0:0_2
Forward
Reverse
Condensing cigar ...
test_92_337_8:0:0_10:0:0_21
Forward
Reverse
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 56
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 56 Got 1
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 6
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 3
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 3 Got 99
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 99 Got 2
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 2 Got 65
Condensing cigar ...
Cigar length didn't match after condense! Expected 19 Got 75
Cigar length didn't match after condense! Expected 56 Got 6
Cigar length didn't match after condense! Expected 1 Got 3
Cigar length didn't match after condense! Expected 6 Got 99
Cigar length didn't match after condense! Expected 3 Got 2
Cigar length didn't match after condense! Expected 99 Got 65
test_147_337_11:1:0_11:1:0_11
Forward
Reverse
Condensing cigar ...
test_149_298_7:0:0_11:0:0_d
Forward
Reverse
Condensing cigar ...
test_184_379_11:1:0_8:1:0_26
Forward
Reverse
Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 6 Got 0
Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 2 Got 89
Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 0 Got 4
Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 89 Got 18
Condensing cigar ...
Cigar length didn't match after condense! Expected 71 Got 160
Cigar flag didn't match! Expected Got 4
Cigar length didn't match after condense! Expected 2 Got 18
FAIL check_unpaired_trim (exit status: 255)
============================================================================
Testsuite summary for ivar 1.4.2
============================================================================
# TOTAL: 19
# PASS: 18
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
============================================================================
See tests/test-suite.log
Please report to gkarthik@scripps.edu
============================================================================
make[5]: *** [Makefile:931: test-suite.log] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[4]: *** [Makefile:1039: check-TESTS] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[3]: *** [Makefile:1238: check-am] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[2]: *** [Makefile:371: check-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: error: make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:16: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:12: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-02-21T19:49:28Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 40156
Build-Time: 68
Distribution: trixie-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 31
Job: ivar_1.4.2+dfsg-3
Machine Architecture: arm64
Package: ivar
Package-Time: 108
Source-Version: 1.4.2+dfsg-3
Space: 40156
Status: attempted
Version: 1.4.2+dfsg-3
--------------------------------------------------------------------------------
Finished at 2024-02-21T19:49:28Z
Build needed 00:01:48, 40156k disk space