ivar →
1.3.1+dfsg-4 →
armhf → 2022-05-01 00:20:28
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| ivar 1.3.1+dfsg-4 (armhf) Sun, 01 May 2022 00:12:18 +0000 |
+==============================================================================+
Package: ivar
Version: 1.3.1+dfsg-4
Source Version: 1.3.1+dfsg-4
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-88d030d9-be93-4f33-9fba-1d6c0d6720a6' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/ivar-pNrRhZ/resolver-uVvVFu' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.0 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.9 MB]
Fetched 26.9 MB in 11s (2431 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: '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 678 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main ivar 1.3.1+dfsg-4 (dsc) [2090 B]
Get:2 http://172.17.4.1/private bookworm-staging/main ivar 1.3.1+dfsg-4 (tar) [630 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main ivar 1.3.1+dfsg-4 (diff) [45.8 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/ivar-pNrRhZ/ivar-1.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ivar-pNrRhZ' 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 [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
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Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [457 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 libicu71
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
librtmp1 libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn11-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 libicu71
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
librtmp1 libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0
libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy zlib1g-dev
0 upgraded, 45 newly installed, 0 to remove and 5 not upgraded.
Need to get 24.4 MB of archives.
After this operation, 78.6 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [880 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38-4 [137 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-1 [33.7 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-1 [1362 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-6 [171 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-6 [510 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.7.1 [195 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-3 [526 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-2 [8857 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.13+dfsg-1+b1 [591 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-6 [1214 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.7.1 [1071 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3 [161 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.82.0-2 [313 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.82.0-2 [389 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.10-2 [55.4 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.10-2 [47.8 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.2.1-1 [52.7 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4 [183 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.13+ds-2 [4049 kB]
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Setting up intltool-debian (0.35.0+20060710.5) ...
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Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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Processing triggers for libc-bin (2.33-7+rpi1) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.38-3+rpi1 dpkg-dev_1.21.7+rpi1 g++-11_11.2.0-20+rpi1 gcc-11_11.2.0-20+rpi1 libc6-dev_2.33-7+rpi1 libstdc++-11-dev_11.2.0-20+rpi1 libstdc++6_12-20220319-1+rpi1 linux-libc-dev_5.16.18-1+rpi1
Package versions: adduser_3.121 apt_2.4.5 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-6 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.5.52 bash_5.1-6 binutils_2.38-3+rpi1 binutils-arm-linux-gnueabihf_2.38-3+rpi1 binutils-common_2.38-3+rpi1 bsdextrautils_2.38-4 bsdutils_1:2.38-4 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-20+rpi1 dash_0.5.11+git20210903+057cd650a4ed-8 debconf_1.5.79 debhelper_13.7.1 debianutils_5.7-0.1 dh-autoreconf_20 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3+b1 dpkg_1.21.7+rpi1 dpkg-dev_1.21.7+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.28-1 file_1:5.41-4 findutils_4.9.0-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-20+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-20+rpi1 gcc-11-base_11.2.0-20+rpi1 gcc-12-base_12-20220319-1+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_0.21-6 gettext-base_0.21-6 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3+b1 gpg_2.2.27-3+b1 gpg-agent_2.2.27-3+b1 gpg-wks-client_2.2.27-3+b1 gpg-wks-server_2.2.27-3+b1 gpgconf_2.2.27-3+b1 gpgsm_2.2.27-3+b1 gpgv_2.2.27-3+b1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.62 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.4.5 libarchive-zip-perl_1.68-1 libasan6_11.2.0-20+rpi1 libassuan0_2.5.5-1 libatomic1_12-20220319-1+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1 libaudit1_1:3.0.7-1+b1 libbinutils_2.38-3+rpi1 libblkid1_2.38-4 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5 libc-bin_2.33-7+rpi1 libc-dev-bin_2.33-7+rpi1 libc6_2.33-7+rpi1 libc6-dev_2.33-7+rpi1 libcap-ng0_0.7.9-2.2+b2 libcap2_1:2.44-1 libcc1-0_12-20220319-1+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.38-3+rpi1 libctf0_2.38-3+rpi1 libcurl3-gnutls_7.82.0-2 libcurl4-gnutls-dev_7.82.0-2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.262 libdebhelper-perl_13.7.1 libdeflate-dev_1.10-2 libdeflate0_1.10-2 libdpkg-perl_1.21.7+rpi1 libelf1_0.186-1 libext2fs2_1.46.5-2 libfakeroot_1.28-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.2.0-20+rpi1 libgcc-s1_12-20220319-1+rpi1 libgcrypt20_1.10.1-2 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.4-2 libgomp1_12-20220319-1+rpi1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.19.2-2+b2 libhogweed6_3.7.3-1 libhts-dev_1.13+ds-2 libhts3_1.13+ds-2 libhtscodecs2_1.2.1-1 libicu71_71.1-2 libidn2-0_2.3.2-2 libisl23_0.24-2 libk5crypto3_1.19.2-2+b2 libkeyutils1_1.6.1-3+rpi1 libkrb5-3_1.19.2-2+b2 libkrb5support0_1.19.2-2+b2 libksba8_1.6.0-2 libldap-2.5-0_2.5.11+dfsg-1+rpi1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2.1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38-4 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncursesw6_6.3-2 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-4 libpcre3_2:8.39-14 libperl5.32_5.32.1-6 libperl5.34_5.34.0-4 libpipeline1_1.5.6-1 libpsl5_0.21.0-1.2 libreadline8_8.1.2-1.2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-4 libsasl2-modules-db_2.1.28+dfsg-4 libseccomp2_2.5.3-2+rpi1+b1 libselinux1_3.3-1+b1 libsemanage-common_3.3-1 libsemanage2_3.3-1+b1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.38-4 libsqlite3-0_3.38.2-1 libss2_1.46.5-2 libssh2-1_1.10.0-3 libssl1.1_1.1.1n-1 libstdc++-11-dev_11.2.0-20+rpi1 libstdc++6_12-20220319-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_250.4-1+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.7-3 libubsan1_12-20220319-1+rpi1 libuchardet0_0.0.7-1 libudev1_250.4-1+rpi1 libunistring2_1.0-1 libuuid1_2.38-4 libxml2_2.9.13+dfsg-1+b1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.16.18-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.2-1 mawk_1.3.4.20200120-3 mount_2.38-4 ncurses-base_6.3-2 ncurses-bin_6.3-2 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-4 perl-base_5.34.0-4 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-4 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1.2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.03-1 tar_1.34+dfsg-1 tzdata_2022a-1 util-linux_2.37.3-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4 zlib1g-dev_1:1.2.11.dfsg-4
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 3.0 (quilt)
Source: ivar
Binary: ivar, ivar-doc
Architecture: any all
Version: 1.3.1+dfsg-4
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: 4.6.0
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:
0618c6cb558643a035fef9579d83f75d42504980 630344 ivar_1.3.1+dfsg.orig.tar.xz
a84687503cd45e3b8cc69fe01fb55aca11316bd0 45776 ivar_1.3.1+dfsg-4.debian.tar.xz
Checksums-Sha256:
1c506993b93b2f6b2fec7328e726bfb91a99a9d36c4b9e0bb174383143a2b192 630344 ivar_1.3.1+dfsg.orig.tar.xz
08f827d196f85b922b780aac228f4743219aafbee44677600848c12f480e4b30 45776 ivar_1.3.1+dfsg-4.debian.tar.xz
Files:
073c189f9294476b494704928099f71f 630344 ivar_1.3.1+dfsg.orig.tar.xz
e8ccdd8ad629a0bb9ea1afd95ca46ffc 45776 ivar_1.3.1+dfsg-4.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.4a6tULSF/trustedkeys.kbx': General error
gpgv: Signature made Wed Sep 22 17:01:16 2021 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./ivar_1.3.1+dfsg-4.dsc
dpkg-source: info: extracting ivar in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking ivar_1.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking ivar_1.3.1+dfsg-4.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 gcc-11.patch
dpkg-source: info: applying gcc-11_2.patch
dpkg-source: info: applying privacy-breach.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=41a23d85cb544dd4a872479b57d3b7e9
JOURNAL_STREAM=8:23099
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-88d030d9-be93-4f33-9fba-1d6c0d6720a6
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c8256
XDG_SESSION_TYPE=unspecified
dpkg-buildpackage
-----------------
Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package ivar
dpkg-buildpackage: info: source version 1.3.1+dfsg-4
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f data/db/test_ref.fa.fai data/test.gap.fa data/test.gap.qual.txt data/test.indel.tsv data/test.masked_primer_indices.txt data/test.trimmed.masked.bam data/test.trimmed.masked.bam.bai data/test.trimmed.sorted.bam.bai data/test.unmapped.sorted.bam.bai
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
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... /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 -Wformat -Werror=format-security -v -g -std=c++11 -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 -Wformat -Werror=format-security -v -g -std=c++11 -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 -Wformat -Werror=format-security -v -g -std=c++11 -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 -Wformat -Werror=format-security -v -g -std=c++11 -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 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cppSupported LTO compression algorithms: zlib zstd
gcc version 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
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-v -I . -I .. -imultilib . -imultiarchCOLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+rpi1)
arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quietCOLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/cc9s1RMl.s
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Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 suffix_tree.cpp -quiet -dumpbase suffix_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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccSvNgus.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
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GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
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ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
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GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
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c773f99eefaaca80e46491b284b7076e
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
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GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
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LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'alignment.'
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Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+rpi1)
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/usr/lib/gcc/arm-linux-gnueabihf/11/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 trim_primer_quality.cpp -quiet -dumpbase trim_primer_quality.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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccccIMHC.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
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GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
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GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
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LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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 -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o remove_reads_from_amplicon.o remove_reads_from_amplicon.cpp
Using built-in specs.
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Target: arm-linux-gnueabihf
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gcc version 11.2.0 (Raspbian 11.2.0-20+rpi1)
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GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
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End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o call_consensus_pileup.o /tmp/cc57cEvd.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o suffix_tree.o /tmp/ccSvNgus.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -Wformat -Werror=format-security -v -g -std=c++11 -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 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccF0IMXf.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
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End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -Wformat -Werror=format-security -v -g -std=c++11 -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 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccvtmuDB.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
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End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o trim_primer_quality.o /tmp/ccccIMHC.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -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 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccfHMnvg.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o remove_reads_from_amplicon.o /tmp/ccTRQSVQ.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -Wformat -Werror=format-security -v -g -std=c++11 -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 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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/lib/gcc/arm-linux-gnueabihf/11/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=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccBMQ7go.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o call_variants.o /tmp/ccF0IMXf.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -Wformat -Werror=format-security -v -g -std=c++11 -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 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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/lib/gcc/arm-linux-gnueabihf/11/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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccuBQrnR.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o allele_functions.o /tmp/ccfHMnvg.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'allele_functions.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -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 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccJUlsxq.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o primer_bed.o /tmp/ccvtmuDB.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o get_masked_amplicons.o /tmp/ccBMQ7go.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -c -o ref_seq.o ref_seq.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/cc9fGyzb.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -Wformat -Werror=format-security -v -g -std=c++11 -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 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/11/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 -std=c++11 -version -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -o /tmp/ccvpuppq.s
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/11"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/11/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/11
/usr/include/arm-linux-gnueabihf/c++/11
/usr/include/c++/11/backward
/usr/lib/gcc/arm-linux-gnueabihf/11/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
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End of search list.
GNU C++11 (Raspbian 11.2.0-20+rpi1) version 11.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 11.2.0, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.1, isl version isl-0.24-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: c773f99eefaaca80e46491b284b7076e
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o interval_tree.o /tmp/ccvpuppq.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o get_common_variants.o /tmp/ccuBQrnR.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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 -mfloat-abi=hard -meabi=5 -o ref_seq.o /tmp/cc9fGyzb.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-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++/11/vector:72,
from /usr/include/c++/11/regex:51,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/regex:51,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘std::vector<gff3_feature> gff3::query_features(uint64_t, std::string)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/regex:51,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/11/bits/vector.tcc: In member function ‘int gff3::read_file(std::string)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -meabi=5 -o parse_gff.o /tmp/ccJUlsxq.s
GNU assembler version 2.38 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.38
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/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' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'parse_gff.'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -v -g -std=c++11 -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o ivar ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread
Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/11/lto-wrapper
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 11.2.0-20+rpi1' --with-bugurl=file:///usr/share/doc/gcc-11/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-11 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --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 11.2.0 (Raspbian 11.2.0-20+rpi1)
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/11/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/11/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'ivar.'
/usr/lib/gcc/arm-linux-gnueabihf/11/collect2 -plugin /usr/lib/gcc/arm-linux-gnueabihf/11/liblto_plugin.so -plugin-opt=/usr/lib/gcc/arm-linux-gnueabihf/11/lto-wrapper -plugin-opt=-fresolution=/tmp/ccctKevh.res -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lgcc --build-id --eh-frame-hdr -dynamic-linker /lib/ld-linux-armhf.so.3 -X --hash-style=gnu --as-needed -m armelf_linux_eabi -o ivar /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crt1.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/11/crtbegin.o -L/usr/lib/gcc/arm-linux-gnueabihf/11 -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/11/../../.. -L/lib/arm-linux-gnueabihf -L/usr/lib/arm-linux-gnueabihf -z relro -z now ivar.o call_consensus_pileup.o alignment.o suffix_tree.o trim_primer_quality.o remove_reads_from_amplicon.o call_variants.o primer_bed.o allele_functions.o get_masked_amplicons.o get_common_variants.o parse_gff.o ref_seq.o interval_tree.o -lhts -lz -lpthread -lhts -lz -lpthread -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/arm-linux-gnueabihf/11/crtend.o /usr/lib/gcc/arm-linux-gnueabihf/11/../../../arm-linux-gnueabihf/crtn.o
COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<<PKGBUILDDIR>>=.' '-fstack-protector-strong' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'ivar.'
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
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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/regex:51,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/11/vector:67,
from /usr/include/c++/11/regex:51,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/11/bits/stl_vector.h: In member function ‘std::vector<gff3_feature> gff3::query_features(uint64_t, std::string)’:
/usr/include/c++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from /usr/include/c++/11/regex:51,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/11/bits/vector.tcc: In member function ‘int gff3::read_file(std::string)’:
/usr/include/c++/11/bits/vector.tcc:121:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
121 | _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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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 -Wformat -Werror=format-security -g -std=c++11 -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -g -std=c++11 -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
make[4]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make check-TESTS
make[4]: Entering directory '/<<PKGBUILDDIR>>/tests'
make[5]: Entering directory '/<<PKGBUILDDIR>>/tests'
FAIL: 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
======================================
ivar 1.3.1: tests/test-suite.log
======================================
# TOTAL: 18
# PASS: 16
# SKIP: 0
# XFAIL: 0
# FAIL: 2
# XPASS: 0
# ERROR: 0
.. contents:: :depth: 2
FAIL: check_primer_trim
=======================
Found 8 primers in BED file
[E::idx_find_and_load] Could not retrieve index file for '../data/test.unmapped.sorted.bam'
test_outside_primer
----
test_20_381_1:0:0_6:0:0_1_150
0-6 6-1 0-5 1-1 0-139
Condensing cigar ...
4-12 0-139
----
test_20_381_1_softclip:0:0_6:0:0_1_150
4-24 0-3 2-2 0-1 1-1 0-4 2-1 6-1 2-1 0-114
Condensing cigar ...
4-33 0-114
----
test_67_308_2:0:0_2:0:0_0_100
----
test_67_308_2:0:0_2:0:0_0_100
----
test_200_349_0:0:0_6:0:0_2_25
----
test_200_349_0:0:0_6:0:0_2_25
----
test_20_381_1:0:0_6:0:0_1_150
0-121 6-1 2-4 0-4 2-1 0-1 6-1 0-1 2-1 0-11 4-6
Condensing cigar ...
0-121 4-23
----
test_20_381_1_softclip:0:0_6:0:0_1_150
0-103 1-1 0-10 1-1 0-13 4-24
Condensing cigar ...
0-103 4-49
----
test_outside_primer
0-41 2-3 0-57 6-1 0-10 6-1 0-39
Incorrect start position
Cigar flag didn't match for 6 ! Expected 2 Got 0
Cigar length didn't match for test_outside_primer ! Expected 3 Got 57
Cigar flag didn't match for 6 ! Expected 0 Got 6
Cigar length didn't match for test_outside_primer ! Expected 57 Got 1
Cigar flag didn't match for 6 ! Expected 6 Got 0
Cigar length didn't match for test_outside_primer ! Expected 1 Got 10
Cigar flag didn't match for 6 ! Expected 0 Got 6
Cigar length didn't match for test_outside_primer ! Expected 10 Got 1
Cigar flag didn't match for 6 ! Expected 6 Got 0
Cigar length didn't match for test_outside_primer ! Expected 1 Got 39
Condensing cigar ...
4-23 0-75 6-1 0-10 6-1 0-39
Cigar length didn't match after condense! Expected 18 Got 75
Cigar flag didn't match! Expected Got 6
Cigar length didn't match after condense! Expected 3 Got 1
Cigar length didn't match after condense! Expected 57 Got 10
Cigar length didn't match after condense! Expected 10 Got 39
----
FAIL check_primer_trim (exit status: 255)
FAIL: check_unpaired_trim
=========================
Found 8 primers in BED file
test_72_280_12:1:0_11:0:0_2
Forward
Reverse
Cigar flag didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 0
Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 1
Cigar flag didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 0 Got 4
Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 1 Got 3
Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 3 Got 2
Cigar length didn't match for test_72_280_12:1:0_11:0:0_2 ! Expected 2 Got 8
Condensing cigar ...
Cigar length didn't match after condense! Expected 93 Got 94
Cigar flag didn't match! Expected Got 4
Cigar length didn't match after condense! Expected 2 Got 13
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 1.3.1
============================================================================
# TOTAL: 18
# PASS: 16
# SKIP: 0
# XFAIL: 0
# FAIL: 2
# XPASS: 0
# ERROR: 0
============================================================================
See tests/test-suite.log
Please report to gkarthik@scripps.edu
============================================================================
make[5]: *** [Makefile:913: test-suite.log] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[4]: *** [Makefile:1021: check-TESTS] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[3]: *** [Makefile:1213: 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 2022-05-01T00:20:24Z
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: 37876
Build-Time: 186
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 270
Job: ivar_1.3.1+dfsg-4
Machine Architecture: armhf
Package: ivar
Package-Time: 486
Source-Version: 1.3.1+dfsg-4
Space: 37876
Status: attempted
Version: 1.3.1+dfsg-4
--------------------------------------------------------------------------------
Finished at 2022-05-01T00:20:24Z
Build needed 00:08:06, 37876k disk space