ivar →
1.4.2+dfsg-3 →
armhf → 2023-12-08 06:18:39
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| ivar 1.4.2+dfsg-3 (armhf) Fri, 08 Dec 2023 06:09:31 +0000 |
+==============================================================================+
Package: ivar
Version: 1.4.2+dfsg-3
Source Version: 1.4.2+dfsg-3
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/trixie-staging-armhf-sbuild-a80221bc-ea60-4105-b264-b75478d39c2f' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.3 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.3 MB in 10s (2908 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'ivar' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/ivar.git
Please use:
git clone https://salsa.debian.org/med-team/ivar.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 721 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main ivar 1.4.2+dfsg-3 (dsc) [2205 B]
Get:2 http://172.17.4.1/private trixie-staging/main ivar 1.4.2+dfsg-3 (tar) [673 kB]
Get:3 http://172.17.4.1/private trixie-staging/main ivar 1.4.2+dfsg-3 (diff) [46.3 kB]
Fetched 721 kB in 0s (7039 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/ivar-46haHa/ivar-1.4.2+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/ivar-46haHa' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-apMPjp/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-apMPjp/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-apMPjp/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ Packages [431 B]
Fetched 2107 B in 0s (10.2 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 57 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (82.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12856 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), libhts-dev
Filtered Build-Depends: debhelper-compat (= 13), libhts-dev
dpkg-deb: building package 'sbuild-build-depends-ivar-dummy' in '/<<BUILDDIR>>/resolver-apMPjp/apt_archive/sbuild-build-depends-ivar-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-ivar-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ Sources [494 B]
Get:5 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ Packages [574 B]
Fetched 2401 B in 0s (12.7 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install ivar build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sgml-base util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils bsdutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libblkid1 libbrotli1
libcurl3-gnutls libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev
libdeflate0 libelf1 libfile-stripnondeterminism-perl libhts-dev libhts3
libhtscodecs2 libicu72 liblzma-dev liblzma5 libmagic-mgc libmagic1 libmount1
libnghttp2-14 libpipeline1 libpsl5 librtmp1 libsmartcols1 libssh2-1
libsub-override-perl libtool libuchardet0 libuuid1 libxml2 m4 man-db mount
po-debconf util-linux util-linux-extra xz-utils zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
libasprintf-dev libgettextpo-dev groff libcurl4-doc libgnutls28-dev
libidn-dev libkrb5-dev libldap2-dev librtmp-dev libssh2-1-dev pkg-config
liblzma-doc cryptsetup-bin libtool-doc gfortran | fortran95-compiler gcj-jdk
m4-doc apparmor less www-browser nfs-common libmail-box-perl dosfstools kbd
util-linux-locales
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl publicsuffix
libltdl-dev uuid-runtime libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libcurl3-gnutls
libcurl4-gnutls-dev libdebhelper-perl libdeflate-dev libdeflate0 libelf1
libfile-stripnondeterminism-perl libhts-dev libhts3 libhtscodecs2 libicu72
liblzma-dev libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
librtmp1 libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4
man-db po-debconf sbuild-build-depends-ivar-dummy zlib1g-dev
The following packages will be upgraded:
bsdutils libblkid1 liblzma5 libmount1 libsmartcols1 libuuid1 mount
util-linux util-linux-extra xz-utils
10 upgraded, 44 newly installed, 0 to remove and 47 not upgraded.
Need to get 25.5 MB of archives.
After this operation, 82.4 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-apMPjp/apt_archive ./ sbuild-build-depends-ivar-dummy 0.invalid.0 [860 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.2-6 [86.5 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.2-6 [102 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf util-linux-extra armhf 2.39.2-6 [135 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.2-6 [1110 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.2-6 [134 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.2-6 [145 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf liblzma5 armhf 5.4.5-0.1 [226 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf libmount1 armhf 2.39.2-6 [167 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.2-6 [28.1 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.2-6 [81.2 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-1 [1358 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:17 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:18 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:19 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:20 http://172.17.4.1/private trixie-staging/main armhf xz-utils armhf 5.4.5-0.1 [499 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.8 [82.1 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.09-4 [9304 B]
Get:31 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:33 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.8 [956 kB]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-3 [195 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.4.0-2+rpi1 [358 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf libcurl4-gnutls-dev armhf 8.4.0-2+rpi1 [441 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf libdeflate-dev armhf 1.18-1 [45.8 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.5.2-1 [60.0 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.18+ds-1 [380 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf liblzma-dev armhf 5.4.5-0.1 [278 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf zlib1g-dev armhf 1:1.2.13.dfsg-3 [901 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libhts-dev armhf 1.18+ds-1 [1539 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking sbuild-build-depends-ivar-dummy (0.invalid.0) ...
Setting up libhtscodecs2:armhf (1.5.2-1) ...
Setting up libpipeline1:armhf (1.5.7-1) ...
Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.2-6) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.8) ...
Setting up libbrotli1:armhf (1.1.0-2) ...
Setting up libnghttp2-14:armhf (1.58.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-14) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up xz-utils (5.4.5-0.1) ...
Setting up autopoint (0.21-14) ...
Setting up autoconf (2.71-3) ...
Setting up liblzma-dev:armhf (5.4.5-0.1) ...
Setting up zlib1g-dev:armhf (1:1.2.13.dfsg-3) ...
Setting up mount (2.39.2-6) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libsub-override-perl (0.09-4) ...
Setting up libssh2-1:armhf (1.11.0-3) ...
Setting up libdeflate-dev:armhf (1.18-1) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up util-linux-extra (2.39.2-6) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-14) ...
Setting up libtool (2.4.7-7) ...
Setting up libcurl3-gnutls:armhf (8.4.0-2+rpi1) ...
Setting up libcurl4-gnutls-dev:armhf (8.4.0-2+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libhts3:armhf (1.18+ds-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.18+ds-1) ...
Setting up man-db (2.12.0-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.11.8) ...
Setting up sbuild-build-depends-ivar-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc-12_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.2 bash_5.2.15-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.2-6 bsdutils_1:2.39.2-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-10+rpi1 cpp-13_13.2.0-5+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.8 debianutils_5.14 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-10+rpi1 g++-13_13.2.0-5+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-10+rpi1 gcc-12-base_12.3.0-10+rpi1 gcc-13_13.2.0-5+rpi1 gcc-13-base_13.2.0-5+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 krb5-locales_1.20.1-5 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-5+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-5+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.2-6 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-1+b1 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_13.2.0-5+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.4.0-2+rpi1 libcurl4-gnutls-dev_8.4.0-2+rpi1 libdb5.3_5.3.28+dfsg2-2 libdebconfclient0_0.271 libdebhelper-perl_13.11.8 libdeflate-dev_1.18-1 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libext2fs2_1.47.0-2 libfakeroot_1.32.1-1 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-10+rpi1 libgcc-13-dev_13.2.0-5+rpi1 libgcc-s1_13.2.0-5+rpi1 libgcrypt20_1.10.2-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.1-4 libgomp1_13.2.0-5+rpi1 libgpg-error0_1.47-2 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhts-dev_1.18+ds-1 libhts3_1.18+ds-1 libhtscodecs2_1.5.2-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.4-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblz4-1_1.9.4-1+rpi1+b1 liblzma-dev_5.4.5-0.1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.2-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231016-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.0-5 libpam-cap_1:2.66-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.36_5.36.0-9 libpipeline1_1.5.7-1 libpsl5_0.21.2-1+b1 libreadline8_8.2-1.3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-3 libsasl2-modules-db_2.1.28+dfsg1-3 libseccomp2_2.5.4-1+rpi1+b1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol1_3.1-1 libsepol2_3.5-1 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.2-6 libsqlite3-0_3.43.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-3 libssl1.1_1.1.1o-1 libssl3_3.0.11-1 libstdc++-12-dev_12.3.0-10+rpi1 libstdc++-13-dev_13.2.0-5+rpi1 libstdc++6_13.2.0-5+rpi1 libsub-override-perl_0.09-4 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20231016-1 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-5+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.2-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-1 mawk_1.3.4.20230808-1 mount_2.39.2-6 nano_7.2-1 ncurses-base_6.4+20231016-1 ncurses-bin_6.4+20231016-1 netbase_6.4 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-9 perl-base_5.36.0-9 perl-modules-5.36_5.36.0-9 pinentry-curses_1.2.1-1 po-debconf_1.0.21+nmu1 raspbian-archive-keyring_20120528.2 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-ivar-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sgml-base_1.31 sysvinit-utils_3.08-3 tar_1.34+dfsg-1.2 tzdata_2023c-10 usrmerge_38 util-linux_2.39.2-6 util-linux-extra_2.39.2-6 xz-utils_5.4.5-0.1 zlib1g_1:1.2.13.dfsg-3 zlib1g-dev_1:1.2.13.dfsg-3
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: Signature made Tue Dec 5 15:15:07 2023 UTC
gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA
gpgv: issuer "emollier@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./ivar_1.4.2+dfsg-3.dsc: no acceptable signature found
dpkg-source: info: extracting ivar in /<<BUILDDIR>>/ivar-1.4.2+dfsg
dpkg-source: info: unpacking ivar_1.4.2+dfsg.orig.tar.xz
dpkg-source: info: unpacking ivar_1.4.2+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying Fix-warning.patch
dpkg-source: info: applying forward-build-options.patch
dpkg-source: info: applying privacy-breach.patch
dpkg-source: info: applying gcc-13.patch
dpkg-source: info: applying gcc-13-2.patch
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-a80221bc-ea60-4105-b264-b75478d39c2f
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package ivar
dpkg-buildpackage: info: source version 1.4.2+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean
dh_clean
debian/rules binary-arch
dh binary-arch
dh_update_autotools_config -a
dh_autoreconf -a
configure.ac:12: installing './compile'
configure.ac:58: installing './config.guess'
configure.ac:58: installing './config.sub'
configure.ac:6: installing './install-sh'
configure.ac:6: installing './missing'
src/Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
dh_auto_configure -a
./configure --build=arm-linux-gnueabihf --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/arm-linux-gnueabihf --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... /usr/bin/mkdir -p
checking for gawk... no
checking for mawk... mawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gawk... (cached) mawk
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ accepts -g... yes
checking for g++ option to enable C++11 features... none needed
checking whether make supports the include directive... yes (GNU style)
checking dependency style of g++... none
checking for gcc... gcc
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... none
checking how to run the C preprocessor... gcc -E
checking for main in -lhts... no
checking for main in -lpthread... no
checking for main in -lz... no
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for unistd.h... (cached) yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int8_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking build system type... arm-unknown-linux-gnueabihf
checking host system type... arm-unknown-linux-gnueabihf
checking for GNU libc compatible malloc... no
checking for GNU libc compatible realloc... no
checking for memmove... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands
dh_auto_build -a
make -j4
make[1]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
make all-recursive
make[2]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
Making all in src
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/src'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o ivar.o ivar.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o call_consensus_pileup.o call_consensus_pileup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o alignment.o alignment.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o suffix_tree.o suffix_tree.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ivar.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ivar.cpp -quietUsing built-in specs.
-dumpbase ivar.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -WallCOLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plusUsing built-in specs.
-quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 alignment.cpp -quiet -dumpbase alignment.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccGCTCku.s
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --ena -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc2pkRVM.s
ble-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_consensus_pileup.cpp -quiet -dumpbase call_consensus_pileup.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc7TJyVu.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, Using built-in specs.
GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
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ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
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GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
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GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
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Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'alignment.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o alignment.o /tmp/ccGCTCku.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
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Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
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GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
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GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
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GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
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Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 remove_reads_from_amplicon.cpp -quiet -dumpbase remove_reads_from_amplicon.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccJJndKG.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/13
/usr/include/arm-linux-gnueabihf/c++/13
/usr/include/c++/13/backward
/usr/lib/gcc/arm-linux-gnueabihf/13/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o call_consensus_pileup.o /tmp/cc7TJyVu.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o suffix_tree.o /tmp/ccEjUsFs.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_consensus_pileup.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'call_consensus_pileup.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o call_variants.o call_variants.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 call_variants.cpp -quiet -dumpbase call_variants.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccdLjHaN.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/13
/usr/include/arm-linux-gnueabihf/c++/13
/usr/include/c++/13/backward
/usr/lib/gcc/arm-linux-gnueabihf/13/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'suffix_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'suffix_tree.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o primer_bed.o primer_bed.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 primer_bed.cpp -quiet -dumpbase primer_bed.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccFx9UCC.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/13
/usr/include/arm-linux-gnueabihf/c++/13
/usr/include/c++/13/backward
/usr/lib/gcc/arm-linux-gnueabihf/13/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o trim_primer_quality.o /tmp/ccFHE8bJ.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o remove_reads_from_amplicon.o /tmp/ccJJndKG.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'trim_primer_quality.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'trim_primer_quality.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o allele_functions.o allele_functions.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 allele_functions.cpp -quiet -dumpbase allele_functions.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cckxkaxB.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/13
/usr/include/arm-linux-gnueabihf/c++/13
/usr/include/c++/13/backward
/usr/lib/gcc/arm-linux-gnueabihf/13/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
/usr/include
End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'remove_reads_from_amplicon.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'remove_reads_from_amplicon.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o get_masked_amplicons.o get_masked_amplicons.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_masked_amplicons.cpp -quiet -dumpbase get_masked_amplicons.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccHBeFny.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
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.
..
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End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o call_variants.o /tmp/ccdLjHaN.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'call_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'call_variants.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o get_common_variants.o get_common_variants.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
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/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 get_common_variants.cpp -quiet -dumpbase get_common_variants.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccHdtgJ8.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
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..
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End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o get_masked_amplicons.o /tmp/ccHBeFny.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_masked_amplicons.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'get_masked_amplicons.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o parse_gff.o parse_gff.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
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/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 parse_gff.cpp -quiet -dumpbase parse_gff.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc9ip7aM.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
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ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
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..
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End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o primer_bed.o /tmp/ccFx9UCC.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'primer_bed.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'primer_bed.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -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 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
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/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 ref_seq.cpp -quiet -dumpbase ref_seq.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/ccIeu4NC.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
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ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
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End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o allele_functions.o /tmp/cckxkaxB.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'allele_functions.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'allele_functions.'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -v -g -Wall -Wextra -Werror -c -o interval_tree.o interval_tree.cpp
Using built-in specs.
COLLECT_GCC=g++
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
/usr/libexec/gcc/arm-linux-gnueabihf/13/cc1plus -quiet -v -I . -I .. -imultilib . -imultiarch arm-linux-gnueabihf -D_GNU_SOURCE -D HAVE_CONFIG_H -D _FORTIFY_SOURCE=2 interval_tree.cpp -quiet -dumpbase interval_tree.cpp -dumpbase-ext .cpp -mfloat-abi=hard -mtls-dialect=gnu -marm -mlibarch=armv6+fp -march=armv6+fp -g -g -O2 -Wdate-time -Wformat=1 -Werror=format-security -Wall -Wextra -Werror -version -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -o /tmp/cc00yQII.s
GNU C++17 (Raspbian 13.2.0-5+rpi1) version 13.2.0 (arm-linux-gnueabihf)
compiled by GNU C version 13.2.0, GMP version 6.3.0, MPFR version 4.2.1, MPC version 1.3.1, isl version isl-0.26-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/13"
ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed/arm-linux-gnueabihf"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/include-fixed"
ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/13/../../../../arm-linux-gnueabihf/include"
#include "..." search starts here:
#include <...> search starts here:
.
..
/usr/include/c++/13
/usr/include/arm-linux-gnueabihf/c++/13
/usr/include/c++/13/backward
/usr/lib/gcc/arm-linux-gnueabihf/13/include
/usr/local/include
/usr/include/arm-linux-gnueabihf
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End of search list.
Compiler executable checksum: 79fa622412d6a2d693f8f046bfe2ebca
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o interval_tree.o /tmp/cc00yQII.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'interval_tree.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'interval_tree.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o get_common_variants.o /tmp/ccHdtgJ8.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'get_common_variants.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'get_common_variants.'
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o ref_seq.o /tmp/ccIeu4NC.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'ref_seq.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'ref_seq.'
In file included from /usr/include/c++/13/regex:59,
from parse_gff.h:6,
from parse_gff.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/13/regex:57:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’,
inlined from ‘std::vector<gff3_feature> gff3::query_features(uint64_t, std::string)’ at parse_gff.cpp:151:20:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘int gff3::read_file(std::string)’ at parse_gff.cpp:139:23:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp'
as -v -I . -I .. -march=armv6+fp -mfloat-abi=hard -meabi=5 -o parse_gff.o /tmp/cc9ip7aM.s
GNU assembler version 2.41 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.41
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-D' 'HAVE_CONFIG_H' '-I' '.' '-I' '..' '-Wdate-time' '-D' '_FORTIFY_SOURCE=2' '-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-c' '-o' 'parse_gff.o' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'parse_gff.'
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Using built-in specs.
COLLECT_GCC=g++
COLLECT_LTO_WRAPPER=/usr/libexec/gcc/arm-linux-gnueabihf/13/lto-wrapper
Target: arm-linux-gnueabihf
Configured with: ../src/configure -v --with-pkgversion='Raspbian 13.2.0-5+rpi1' --with-bugurl=file:///usr/share/doc/gcc-13/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-13 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/libexec --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 13.2.0 (Raspbian 13.2.0-5+rpi1)
MAKEFLAGS=w -j4
COMPILER_PATH=/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/13/:/usr/libexec/gcc/arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/
LIBRARY_PATH=/usr/lib/gcc/arm-linux-gnueabihf/13/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/:/usr/lib/gcc/arm-linux-gnueabihf/13/../../../:/lib/arm-linux-gnueabihf/:/lib/:/usr/lib/arm-linux-gnueabihf/:/usr/lib/
COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'ivar.'
/usr/libexec/gcc/arm-linux-gnueabihf/13/collect2 -plugin /usr/libexec/gcc/arm-linux-gnueabihf/13/liblto_plugin.so -plugin-opt=/usr/libexec/gcc/arm-linux-gnueabihf/13/lto-wrapper -plugin-opt=-fresolution=/tmp/ccNsYgKM.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/13/../../../arm-linux-gnueabihf/crt1.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crti.o /usr/lib/gcc/arm-linux-gnueabihf/13/crtbegin.o -L/usr/lib/gcc/arm-linux-gnueabihf/13 -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf -L/usr/lib/gcc/arm-linux-gnueabihf/13/../../.. -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/13/crtend.o /usr/lib/gcc/arm-linux-gnueabihf/13/../../../arm-linux-gnueabihf/crtn.o
COLLECT_GCC_OPTIONS='-g' '-O2' '-ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=.' '-fstack-protector-strong' '-fstack-clash-protection' '-Wformat=1' '-Werror=format-security' '-v' '-g' '-Wall' '-Wextra' '-Werror' '-o' 'ivar' '-shared-libgcc' '-mfloat-abi=hard' '-mtls-dialect=gnu' '-marm' '-mlibarch=armv6+fp' '-march=armv6+fp' '-dumpdir' 'ivar.'
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/src'
Making all in tests
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
make[2]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
make[1]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
dh_auto_test --no-parallel
make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1
make[2]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
Making check in src
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/src'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/src'
Making check in tests
make[3]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
make check_primer_trim check_trim check_quality_trim check_consensus check_allele_depth check_consensus_threshold check_consensus_min_depth check_consensus_seq_id check_primer_bed check_getmasked check_removereads check_variants check_common_variants check_unpaired_trim check_primer_trim_edge_cases check_isize_trim check_interval_tree check_amplicon_search check_consensus_min_insert_threshold
make[4]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_trim.o test_primer_trim.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/trim_primer_quality.o ../src/trim_primer_quality.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/primer_bed.o ../src/primer_bed.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/interval_tree.o ../src/interval_tree.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim test_primer_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_trim.o test_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_trim test_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o check_quality_trim.o check_quality_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_quality_trim check_quality_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_call_consensus_from_plup.o test_call_consensus_from_plup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/call_consensus_pileup.o ../src/call_consensus_pileup.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/allele_functions.o ../src/allele_functions.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus test_call_consensus_from_plup.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_allele_depth.o test_allele_depth.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_allele_depth test_allele_depth.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_threshold.o test_consensus_threshold.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_threshold test_consensus_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_min_depth.o test_consensus_min_depth.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_depth test_consensus_min_depth.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_seq_id.o test_consensus_seq_id.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_seq_id test_consensus_seq_id.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_bed.o test_primer_bed.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_bed test_primer_bed.o ../src/primer_bed.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_getmasked.o test_getmasked.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/get_masked_amplicons.o ../src/get_masked_amplicons.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_getmasked test_getmasked.o ../src/get_masked_amplicons.o ../src/primer_bed.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_removereads.o test_removereads.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/remove_reads_from_amplicon.o ../src/remove_reads_from_amplicon.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_removereads test_removereads.o ../src/remove_reads_from_amplicon.o ../src/primer_bed.o ../src/trim_primer_quality.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_variants.o test_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/call_variants.o ../src/call_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/parse_gff.o ../src/parse_gff.cpp
In file included from /usr/include/c++/13/regex:59,
from ../src/parse_gff.h:6,
from ../src/parse_gff.cpp:1:
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
445 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/13/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const gff3_feature&}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’:
/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type ‘std::vector<gff3_feature>::iterator’ changed in GCC 7.1
In file included from /usr/include/c++/13/regex:57:
In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’,
inlined from ‘std::vector<gff3_feature> gff3::query_features(uint64_t, std::string)’ at ../src/parse_gff.cpp:151:20:
/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
1289 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function ‘std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {gff3_feature}; _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’,
inlined from ‘void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = gff3_feature; _Alloc = std::allocator<gff3_feature>]’ at /usr/include/c++/13/bits/stl_vector.h:1296:21,
inlined from ‘int gff3::read_file(std::string)’ at ../src/parse_gff.cpp:139:23:
/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<gff3_feature*, std::vector<gff3_feature> >’ changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/ref_seq.o ../src/ref_seq.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_variants test_variants.o ../src/call_variants.o ../src/allele_functions.o ../src/parse_gff.o ../src/ref_seq.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_common_variants.o test_common_variants.cpp
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o ../src/get_common_variants.o ../src/get_common_variants.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_common_variants test_common_variants.o ../src/get_common_variants.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_unpaired_trim.o test_unpaired_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_unpaired_trim test_unpaired_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_primer_trim_edge_cases.o test_primer_trim_edge_cases.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_primer_trim_edge_cases test_primer_trim_edge_cases.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_isize_trim.o test_isize_trim.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_isize_trim test_isize_trim.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_interval_tree.o test_interval_tree.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_interval_tree test_interval_tree.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_amplicon_search.o test_amplicon_search.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_amplicon_search test_amplicon_search.o ../src/trim_primer_quality.o ../src/primer_bed.o ../src/interval_tree.o -lhts -lz -lpthread
g++ -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -c -o test_consensus_min_insert_threshold.o test_consensus_min_insert_threshold.cpp
g++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/ivar-1.4.2+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -g -Wall -Wextra -Werror -Wl,-z,relro -Wl,-z,now -o check_consensus_min_insert_threshold test_consensus_min_insert_threshold.o ../src/call_consensus_pileup.o ../src/allele_functions.o -lhts -lz -lpthread
make[4]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
make check-TESTS
make[4]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
make[5]: Entering directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
PASS: check_primer_trim
PASS: check_trim
PASS: check_quality_trim
PASS: check_consensus
PASS: check_allele_depth
PASS: check_consensus_threshold
PASS: check_consensus_min_depth
PASS: check_consensus_seq_id
PASS: check_primer_bed
PASS: check_getmasked
PASS: check_removereads
PASS: check_variants
PASS: check_common_variants
FAIL: check_unpaired_trim
PASS: check_primer_trim_edge_cases
PASS: check_isize_trim
PASS: check_interval_tree
PASS: check_amplicon_search
PASS: check_consensus_min_insert_threshold
======================================
ivar 1.4.2: tests/test-suite.log
======================================
# TOTAL: 19
# PASS: 18
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
.. contents:: :depth: 2
FAIL: check_unpaired_trim
=========================
Found 8 primers in BED file
test_72_280_12:1:0_11:0:0_2
Forward
Reverse
Condensing cigar ...
test_92_337_8:0:0_10:0:0_21
Forward
Reverse
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 56
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 56 Got 1
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 1 Got 6
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 3
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 3 Got 99
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 0 Got 6
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 99 Got 2
Cigar flag didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 6 Got 0
Cigar length didn't match for test_92_337_8:0:0_10:0:0_21 ! Expected 2 Got 65
Condensing cigar ...
Cigar length didn't match after condense! Expected 19 Got 75
Cigar length didn't match after condense! Expected 56 Got 6
Cigar length didn't match after condense! Expected 1 Got 3
Cigar length didn't match after condense! Expected 6 Got 99
Cigar length didn't match after condense! Expected 3 Got 2
Cigar length didn't match after condense! Expected 99 Got 65
test_147_337_11:1:0_11:1:0_11
Forward
Reverse
Condensing cigar ...
test_149_298_7:0:0_11:0:0_d
Forward
Reverse
Condensing cigar ...
test_184_379_11:1:0_8:1:0_26
Forward
Reverse
Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 6 Got 0
Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 2 Got 89
Cigar flag didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 0 Got 4
Cigar length didn't match for test_184_379_11:1:0_8:1:0_26 ! Expected 89 Got 18
Condensing cigar ...
Cigar length didn't match after condense! Expected 71 Got 160
Cigar flag didn't match! Expected Got 4
Cigar length didn't match after condense! Expected 2 Got 18
FAIL check_unpaired_trim (exit status: 255)
============================================================================
Testsuite summary for ivar 1.4.2
============================================================================
# TOTAL: 19
# PASS: 18
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
============================================================================
See tests/test-suite.log
Please report to gkarthik@scripps.edu
============================================================================
make[5]: *** [Makefile:931: test-suite.log] Error 1
make[5]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
make[4]: *** [Makefile:1039: check-TESTS] Error 2
make[4]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
make[3]: *** [Makefile:1238: check-am] Error 2
make[3]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg/tests'
make[2]: *** [Makefile:371: check-recursive] Error 1
make[2]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
dh_auto_test: error: make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 returned exit code 2
make[1]: *** [debian/rules:16: override_dh_auto_test] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/ivar-1.4.2+dfsg'
make: *** [debian/rules:12: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2023-12-08T06:18:38Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 40084
Build-Time: 181
Distribution: trixie-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 346
Job: ivar_1.4.2+dfsg-3
Machine Architecture: armhf
Package: ivar
Package-Time: 547
Source-Version: 1.4.2+dfsg-3
Space: 40084
Status: attempted
Version: 1.4.2+dfsg-3
--------------------------------------------------------------------------------
Finished at 2023-12-08T06:18:38Z
Build needed 00:09:07, 40084k disk space