ivar →
1.3+dfsg-1 →
armhf → 2021-09-01 00:09:11
sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019
+==============================================================================+
| ivar 1.3+dfsg-1 (armhf) Wed, 01 Sep 2021 00:03:25 +0000 |
+==============================================================================+
Package: ivar
Version: 1.3+dfsg-1
Source Version: 1.3+dfsg-1
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-e0ebad03-c610-45b3-9432-96651fbbb00e' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/ivar-Vjasyo/resolver-Kkc9SD' with '<<RESOLVERDIR>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bookworm-staging/main Sources [12.3 MB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf Packages [13.4 MB]
Fetched 25.7 MB in 11s (2391 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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 675 kB of source archives.
Get:1 http://172.17.0.1/private bookworm-staging/main ivar 1.3+dfsg-1 (dsc) [2036 B]
Get:2 http://172.17.0.1/private bookworm-staging/main ivar 1.3+dfsg-1 (tar) [630 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main ivar 1.3+dfsg-1 (diff) [43.0 kB]
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Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/ivar-Vjasyo/ivar-1.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ivar-Vjasyo' 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 [461 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...
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 libicu67 liblzma-dev
libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5 librtmp1
libsigsegv2 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db po-debconf sensible-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
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 libicu67 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 sensible-utils zlib1g-dev
0 upgraded, 45 newly installed, 0 to remove and 43 not upgraded.
Need to get 23.3 MB of archives.
After this operation, 74.8 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://172.17.0.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-1 [135 kB]
Get:3 http://172.17.0.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.0.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:5 http://172.17.0.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:6 http://172.17.0.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.0.1/private bookworm-staging/main armhf sensible-utils all 0.0.16 [21.4 kB]
Get:8 http://172.17.0.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:9 http://172.17.0.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:10 http://172.17.0.1/private bookworm-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:11 http://172.17.0.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:12 http://172.17.0.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:13 http://172.17.0.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:14 http://172.17.0.1/private bookworm-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:15 http://172.17.0.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:16 http://172.17.0.1/private bookworm-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:17 http://172.17.0.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:18 http://172.17.0.1/private bookworm-staging/main armhf libdebhelper-perl all 13.4.1 [191 kB]
Get:19 http://172.17.0.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:20 http://172.17.0.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:21 http://172.17.0.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:22 http://172.17.0.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:23 http://172.17.0.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.0-1 [26.3 kB]
Get:24 http://172.17.0.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.0-1 [15.4 kB]
Get:25 http://172.17.0.1/private bookworm-staging/main armhf libelf1 armhf 0.185-2 [168 kB]
Get:26 http://172.17.0.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:27 http://172.17.0.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:28 http://172.17.0.1/private bookworm-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.7 [580 kB]
Get:29 http://172.17.0.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:30 http://172.17.0.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:31 http://172.17.0.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:32 http://172.17.0.1/private bookworm-staging/main armhf debhelper all 13.4.1 [1039 kB]
Get:33 http://172.17.0.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:34 http://172.17.0.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:35 http://172.17.0.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:36 http://172.17.0.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:37 http://172.17.0.1/private bookworm-staging/main armhf libssh2-1 armhf 1.9.0-3 [151 kB]
Get:38 http://172.17.0.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.74.0-1.3 [301 kB]
Get:39 http://172.17.0.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.74.0-1.3 [375 kB]
Get:40 http://172.17.0.1/private bookworm-staging/main armhf libdeflate0 armhf 1.7-2 [44.1 kB]
Get:41 http://172.17.0.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.7-2 [40.5 kB]
Get:42 http://172.17.0.1/private bookworm-staging/main armhf libhts3 armhf 1.11-4 [324 kB]
Get:43 http://172.17.0.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2 [219 kB]
Get:44 http://172.17.0.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:45 http://172.17.0.1/private bookworm-staging/main armhf libhts-dev armhf 1.11-4 [3815 kB]
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update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any 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_2.35.2-2+rpi1 dpkg-dev_1.20.9+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-13+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.46-4+rpi1
Package versions: adduser_3.118 apt_2.2.4 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11.1+rpi1 base-passwd_3.5.51 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.37.2-1 bsdutils_1:2.36.1-8 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.77 debhelper_13.4.1 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.2-2 fakeroot_1.25.3-1.1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.3.0-22+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-10 libapt-pkg6.0_2.2.4 libarchive-zip-perl_1.68-1 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblkid1_2.36.1-8 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.31-13+rpi1 libc-dev-bin_2.31-13+rpi1 libc6_2.31-13+rpi1 libc6-dev_2.31-13+rpi1 libcap-ng0_0.7.9-2.2+b1 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-2 libcrypt-dev_1:4.4.18-4 libcrypt1_1:4.4.18-4 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl3-gnutls_7.74.0-1.3 libcurl4-gnutls-dev_7.74.0-1.3 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.4.1 libdeflate-dev_1.7-2 libdeflate0_1.7-2 libdpkg-perl_1.20.9+rpi1 libelf1_0.185-2 libext2fs2_1.46.2-2 libfakeroot_1.25.3-1.1 libffi7_3.3-6 libfile-stripnondeterminism-perl_1.12.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-6 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-5 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-6 libhogweed6_3.7.3-1 libhts-dev_1.11-4 libhts3_1.11-4 libicu67_67.1-7 libidn2-0_2.3.0-5 libisl23_0.23-1 libk5crypto3_1.18.3-6 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-6 libkrb5support0_1.18.3-6 libksba8_1.5.0-3 libldap-2.4-2_2.4.57+dfsg-3 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma-dev_5.2.5-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.36.1-8 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20201114-2 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_0.23.22-1 libpam-modules_1.4.0-9 libpam-modules-bin_1.4.0-9 libpam-runtime_1.4.0-9 libpam0g_1.4.0-9 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-4+deb11u1 libpipeline1_1.5.3-1 libpsl5_0.21.0-1.2 libreadline8_8.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libsmartcols1_2.36.1-8 libsqlite3-0_3.34.1-3 libss2_1.46.2-2 libssh2-1_1.9.0-3 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-6+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-6+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-8 libxml2_2.9.10+dfsg-6.7 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1+rpi1 linux-libc-dev_5.10.46-4+rpi1 login_1:4.8.1-1 logsave_1.46.2-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 mount_2.36.1-8 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-4+deb11u1 perl-base_5.32.1-4+deb11u1 perl-modules-5.32_5.32.1-5 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.16 sysvinit-utils_2.96-7 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-8 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| 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+dfsg-1
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/andersen-lab/ivar
Standards-Version: 4.5.1
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:
743fcaeac5b42311cb0d7d180932c8caeb0fcb6d 630292 ivar_1.3+dfsg.orig.tar.xz
4ed491f61b0494756f4c9494f6e529a3c271449f 42988 ivar_1.3+dfsg-1.debian.tar.xz
Checksums-Sha256:
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deff74cce3a60d44b99dc7d1e6d784c42b1c9c78a02496562cab29ef093b12f6 42988 ivar_1.3+dfsg-1.debian.tar.xz
Files:
c54b862be202ef61b52d8dd7a69908ce 630292 ivar_1.3+dfsg.orig.tar.xz
9a75e6c5f1a30d33bea62971f4e3d017 42988 ivar_1.3+dfsg-1.debian.tar.xz
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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.jgciQn6J/trustedkeys.kbx': General error
gpgv: Signature made Sun Dec 13 22:44:37 2020 UTC
gpgv: using RSA key E50AFD55ADD27AAB97163A8B21D20589974B3E96
gpgv: issuer "tmancill@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./ivar_1.3+dfsg-1.dsc
dpkg-source: info: extracting ivar in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking ivar_1.3+dfsg.orig.tar.xz
dpkg-source: info: unpacking ivar_1.3+dfsg-1.debian.tar.xz
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=e040c44591bf400793155c77e2e04554
JOURNAL_STREAM=8:7708138
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-e0ebad03-c610-45b3-9432-96651fbbb00e
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c78502
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+dfsg-1
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: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 thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking 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 we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking 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 grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... 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 for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... no
checking for stdlib.h... (cached) yes
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 -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 -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 -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 -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 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -IUsing built-in specs.
. -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quiet -dumpbase ivar.cpp -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip ivar.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccW04vM8.s
Supported LTO compression algorithms: zlib zstd
gcc version 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC=g++
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip call_consensus_pileup.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccdOcyqf.s
Target: arm-linux-gnueabihf
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GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
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GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
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GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
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GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
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GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
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GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
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GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
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GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
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COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/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 -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip call_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccLmTk9l.s
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
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.
..
/usr/include/c++/10
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End of search list.
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: db87415434a7c3b71e7ddc297314da99
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/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 -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip primer_bed.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccoHhCQs.s
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/10
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End of search list.
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: db87415434a7c3b71e7ddc297314da99
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o trim_primer_quality.o /tmp/ccdXQMeN.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o remove_reads_from_amplicon.o /tmp/ccJZbDo1.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/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 -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip allele_functions.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccOSpqBM.s
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/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 -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip get_masked_amplicons.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccug99eR.s
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/10
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End of search list.
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/10
/usr/include/arm-linux-gnueabihf/c++/10
/usr/include/c++/10/backward
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/usr/local/include
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End of search list.
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: db87415434a7c3b71e7ddc297314da99
Compiler executable checksum: db87415434a7c3b71e7ddc297314da99
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o primer_bed.o /tmp/ccoHhCQs.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -v -g -std=c++11 -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o get_masked_amplicons.o /tmp/ccug99eR.s
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o allele_functions.o /tmp/ccOSpqBM.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
Using built-in specs.
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/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 -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip get_common_variants.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccW7gdZ8.s
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/10
/usr/include/arm-linux-gnueabihf/c++/10
/usr/include/c++/10/backward
/usr/lib/gcc/arm-linux-gnueabihf/10/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: db87415434a7c3b71e7ddc297314da99
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/cc1plusMAKEFLAGS=w -j4
-quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_HCOMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
-D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip parse_gff.o -g -Wdate-timeLIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
-Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccay9Hdu.s
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/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 -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip ref_seq.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/cc30oF5B.s
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/10
/usr/include/arm-linux-gnueabihf/c++/10
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/usr/local/include
/usr/include/arm-linux-gnueabihf
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End of search list.
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/10
/usr/include/arm-linux-gnueabihf/c++/10
/usr/include/c++/10/backward
/usr/lib/gcc/arm-linux-gnueabihf/10/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: db87415434a7c3b71e7ddc297314da99
Compiler executable checksum: db87415434a7c3b71e7ddc297314da99
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o call_variants.o /tmp/ccLmTk9l.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -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 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/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 -mfloat-abi=hard -mfpu=vfp -mtls-dialect=gnu -marm -march=armv6+fp -auxbase-strip interval_tree.o -g -Wdate-time -Wall -Wextra -Werror -std=c++11 -version -o /tmp/ccD9SNWP.s
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/10"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/10/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/10
/usr/include/arm-linux-gnueabihf/c++/10
/usr/include/c++/10/backward
/usr/lib/gcc/arm-linux-gnueabihf/10/include
/usr/local/include
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End of search list.
GNU C++11 (Raspbian 10.2.1-6+rpi1) version 10.2.1 20210110 (arm-linux-gnueabihf)
compiled by GNU C version 10.2.1 20210110, GMP version 6.2.1, MPFR version 4.1.0, MPC version 1.2.0, isl version isl-0.23-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: db87415434a7c3b71e7ddc297314da99
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o get_common_variants.o /tmp/ccW7gdZ8.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o interval_tree.o /tmp/ccD9SNWP.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o ref_seq.o /tmp/cc30oF5B.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/regex:51,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/10/bits/stl_vector.h:558:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
558 | std::__uninitialized_copy_a(__x.begin(), __x.end(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
559 | this->_M_impl._M_start,
| ~~~~~~~~~~~~~~~~~~~~~~~
560 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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++/10/memory:66,
from /usr/include/c++/10/regex:45,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/regex:51,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/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>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:66,
from /usr/include/c++/10/regex:45,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*]’:
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/regex:51,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/10/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++/10/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>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:66,
from /usr/include/c++/10/regex:45,
from parse_gff.h:4,
from parse_gff.cpp:1:
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator<gff3_feature>]’:
/usr/include/c++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
346 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*]’:
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
as -v -I . -I .. -march=armv6 -mfloat-abi=hard -mfpu=vfp -meabi=5 -o parse_gff.o /tmp/ccay9Hdu.s
GNU assembler version 2.35.2 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.35.2
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/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' '-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
g++ -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/10/lto-wrapper
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 10.2.1-6+rpi1' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --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 --with-fpu=vfp --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 10.2.1 20210110 (Raspbian 10.2.1-6+rpi1)
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/10/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/10/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
/usr/lib/gcc/arm-linux-gnueabihf/10/collect2 -plugin /usr/lib/gcc/arm-linux-gnueabihf/10/liblto_plugin.so -plugin-opt=/usr/lib/gcc/arm-linux-gnueabihf/10/lto-wrapper -plugin-opt=-fresolution=/tmp/ccf7HJAK.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/10/../../../arm-linux-gnueabihf/crt1.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/10/crtbegin.o -L/usr/lib/gcc/arm-linux-gnueabihf/10 -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/10/../../.. -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/10/crtend.o /usr/lib/gcc/arm-linux-gnueabihf/10/../../../arm-linux-gnueabihf/crtn.o
COLLECT_GCC_OPTIONS='-v' '-g' '-std=c++11' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mfpu=vfp' '-mtls-dialect=gnu' '-marm' '-march=armv6+fp'
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 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 -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 -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp
g++ -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 -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp
g++ -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp
g++ -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp
g++ -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 -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/regex:51,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/10/bits/stl_vector.h: In copy constructor ‘std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/10/bits/stl_vector.h:558:31: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
558 | std::__uninitialized_copy_a(__x.begin(), __x.end(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
559 | this->_M_impl._M_start,
| ~~~~~~~~~~~~~~~~~~~~~~~
560 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/10/bits/stl_vector.h:1198:21: 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++/10/memory:66,
from /usr/include/c++/10/regex:45,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/regex:51,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/10/bits/vector.tcc:121:21: 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)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/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>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:66,
from /usr/include/c++/10/regex:45,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*]’:
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/regex:51,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/10/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++/10/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>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:66,
from /usr/include/c++/10/regex:45,
from ../src/parse_gff.h:4,
from ../src/parse_gff.cpp:1:
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = gff3_feature*; _ForwardIterator = gff3_feature*; _Allocator = std::allocator<gff3_feature>]’:
/usr/include/c++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
346 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; _Tp = gff3_feature]’:
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In function ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*]’:
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h: In static member function ‘static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<gff3_feature*>; _ForwardIterator = gff3_feature*; bool _TrivialValueTypes = false]’:
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
84 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:84:9: note: parameter passing for argument of type ‘std::move_iterator<gff3_feature*>’ changed in GCC 7.1
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -std=c++11 -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp
g++ -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 -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 -std=c++11 -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp
g++ -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 -std=c++11 -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp
g++ -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: 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
============================================================================
# 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:904: test-suite.log] Error 1
make[5]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[4]: *** [Makefile:1012: check-TESTS] Error 2
make[4]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[3]: *** [Makefile:1205: check-am] Error 2
make[3]: Leaving directory '/<<PKGBUILDDIR>>/tests'
make[2]: *** [Makefile:362: check-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test: error: make -j1 check VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:12: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2021-09-01T00:09:09Z
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: 25684
Build-Time: 99
Distribution: bookworm-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 218
Job: ivar_1.3+dfsg-1
Machine Architecture: armhf
Package: ivar
Package-Time: 344
Source-Version: 1.3+dfsg-1
Space: 25684
Status: attempted
Version: 1.3+dfsg-1
--------------------------------------------------------------------------------
Finished at 2021-09-01T00:09:09Z
Build needed 00:05:44, 25684k disk space