sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org

+==============================================================================+
| lumpy-sv 0.3.1+dfsg-8 (i386)                 Wed, 05 Nov 2025 17:34:36 +0000 |
+==============================================================================+

Package: lumpy-sv
Version: 0.3.1+dfsg-8
Source Version: 0.3.1+dfsg-8
Distribution: unstable
Machine Architecture: arm64
Host Architecture: i386
Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any

Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.9vsHqKubcR...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/lumpy-sv-ZaJdIl/resolver-XN187k' with '<<RESOLVERDIR>>'

+------------------------------------------------------------------------------+
| Update chroot                                                                |
+------------------------------------------------------------------------------+

Get:1 http://mirror.einval.org/debian unstable InRelease [176 kB]
Get:2 http://mirror.einval.org/debian unstable/main Sources [11.2 MB]
Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [10.1 MB]
Get:4 http://mirror.einval.org/debian unstable/main i386 Packages [9961 kB]
Fetched 31.4 MB in 7s (4345 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
  base-passwd linux-libc-dev
2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 2589 kB of archives.
After this operation, 10.2 kB of additional disk space will be used.
Get:1 http://mirror.einval.org/debian unstable/main arm64 base-passwd arm64 3.6.8 [54.0 kB]
Get:2 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev all 6.17.7-1 [2535 kB]
Preconfiguring packages ...
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(Reading database ... 12024 files and directories currently installed.)
Preparing to unpack .../base-passwd_3.6.8_arm64.deb ...
Unpacking base-passwd (3.6.8) over (3.6.7) ...
Setting up base-passwd (3.6.8) ...
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Preparing to unpack .../linux-libc-dev_6.17.7-1_all.deb ...
Unpacking linux-libc-dev (6.17.7-1) over (6.17.6-1) ...
Setting up linux-libc-dev (6.17.7-1) ...

+------------------------------------------------------------------------------+
| Fetch source files                                                           |
+------------------------------------------------------------------------------+


Check APT
---------

Checking available source versions...

Download source files with APT
------------------------------

Reading package lists...
NOTICE: 'lumpy-sv' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/lumpy-sv.git
Please use:
git clone https://salsa.debian.org/med-team/lumpy-sv.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 39.4 MB of source archives.
Get:1 http://mirror.einval.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (dsc) [1594 B]
Get:2 http://mirror.einval.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (tar) [112 kB]
Get:3 http://mirror.einval.org/debian unstable/main lumpy-sv 0.3.1+dfsg-8 (diff) [39.3 MB]
Fetched 39.4 MB in 0s (97.1 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/lumpy-sv-ZaJdIl/lumpy-sv-0.3.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/lumpy-sv-ZaJdIl' with '<<BUILDDIR>>'

+------------------------------------------------------------------------------+
| Install package build dependencies                                           |
+------------------------------------------------------------------------------+


Setup apt archive
-----------------

Merged Build-Depends: debhelper-compat (= 13), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386
Filtered Build-Depends: debhelper-compat (= 13), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-i386:arm64, libc-dev:i386, libstdc++-dev:i386
dpkg-deb: warning: root directory /<<RESOLVERDIR>>/sbuild-build-depends-main-dummy has unusual owner or group 998:999
dpkg-deb: hint: you might need to pass --root-owner-group, see <https://wiki.debian.org/Teams/Dpkg/RootlessBuilds> for further details
dpkg-deb: warning: ignoring 1 warning about the control file(s)
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [834 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [876 B]
Fetched 2319 B in 0s (110 kB/s)
Reading package lists...
Reading package lists...

Install main build dependencies (apt-based resolver)
----------------------------------------------------

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Execute external solver...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils-i686-linux-gnu
  bsdextrautils comerr-dev:i386 cpp-15-i686-linux-gnu cpp-i686-linux-gnu
  crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism
  dwz fakeroot file g++-15-i686-linux-gnu g++-i686-linux-gnu gcc-15-base:i386
  gcc-15-cross-base gcc-15-i686-linux-gnu gcc-15-i686-linux-gnu-base
  gcc-i686-linux-gnu gettext gettext-base groff-base intltool-debian
  krb5-multidev:i386 libarchive-zip-perl libasan8:i386 libasan8-i386-cross
  libatomic1:i386 libatomic1-i386-cross libbamtools-dev:i386
  libbamtools2.5.3:i386 libbrotli-dev:i386 libbrotli1:i386 libbz2-1.0:i386
  libbz2-dev:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross
  libc6-i386-cross libcom-err2:i386 libcrypt-dev:i386 libcrypt1:i386
  libcurl3t64-gnutls:i386 libcurl4-gnutls-dev:i386 libdb5.3t64:i386
  libdebhelper-perl libdeflate-dev:i386 libdeflate0:i386 libelf1t64
  libevent-2.1-7t64:i386 libfakeroot libfastahack-dev:i386 libfastahack0:i386
  libffi8:i386 libfile-stripnondeterminism-perl libgcc-15-dev:i386
  libgcc-15-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgmp-dev:i386
  libgmp10:i386 libgmpxx4ldbl:i386 libgnutls-dane0t64:i386
  libgnutls-openssl27t64:i386 libgnutls28-dev:i386 libgnutls30t64:i386
  libgomp1:i386 libgomp1-i386-cross libgssapi-krb5-2:i386 libgssrpc4t64:i386
  libgzstream-dev:i386 libgzstream0:i386 libhogweed6t64:i386 libhts-dev:i386
  libhts3t64:i386 libhtscodecs2:i386 libidn2-0:i386 libidn2-dev:i386
  libitm1:i386 libitm1-i386-cross libk5crypto3:i386 libkadm5clnt-mit12:i386
  libkadm5srv-mit12:i386 libkdb5-10t64:i386 libkeyutils1:i386 libkrb5-3:i386
  libkrb5-dev:i386 libkrb5support0:i386 libldap-dev:i386 libldap2:i386
  liblzma-dev:i386 liblzma5:i386 libmagic-mgc libmagic1t64 libncurses6:i386
  libnettle8t64:i386 libnghttp2-14:i386 libnghttp2-dev:i386 libnghttp3-9:i386
  libnghttp3-dev:i386 libngtcp2-16:i386 libngtcp2-crypto-gnutls-dev:i386
  libngtcp2-crypto-gnutls8:i386 libngtcp2-dev:i386 libp11-kit-dev:i386
  libp11-kit0:i386 libpipeline1 libpkgconf3 libpsl-dev:i386 libpsl5t64:i386
  libquadmath0:i386 libquadmath0-i386-cross librtmp-dev:i386 librtmp1:i386
  libsasl2-2:i386 libsasl2-modules-db:i386 libsqlite3-0:i386
  libsqlite3-dev:i386 libssh2-1-dev:i386 libssh2-1t64:i386 libssl-dev:i386
  libssl3t64:i386 libstdc++-15-dev:i386 libstdc++-15-dev-i386-cross
  libstdc++6:i386 libstdc++6-i386-cross libtasn1-6:i386 libtasn1-6-dev:i386
  libtinfo6:i386 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0
  libunbound8:i386 libunistring5 libunistring5:i386 libxml2-16
  libzstd-dev:i386 libzstd1:i386 linux-libc-dev-i386-cross m4 man-db
  nettle-dev:i386 pkgconf:i386 pkgconf-bin po-debconf samtools:i386
  sensible-utils zlib1g:i386 zlib1g-dev:i386
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc doc-base:i386
  gcc-15-locales cpp-15-doc cpp-doc dh-make gcc-15-doc manpages-dev flex bison
  gdb-i686-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev
  gnulib-l10n groff krb5-doc:i386 libbamtools-doc:i386 glibc-doc:i386
  libc-l10n:i386 locales:i386 libnss-nis:i386 libnss-nisplus:i386
  manpages-dev:i386 libcurl4-doc:i386 libidn-dev:i386 gmp-doc:i386
  libgmp10-doc:i386 libmpfr-dev:i386 dns-root-data:i386 gnutls-bin:i386
  gnutls-doc:i386 krb5-user:i386 liblzma-doc:i386 libnghttp2-doc:i386
  p11-kit-doc:i386 sqlite3-doc:i386 libssl-doc:i386 libstdc++-15-doc:i386
  libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser
  libmail-box-perl cwltool:i386
Recommended packages:
  curl | wget | lynx bzip2-doc:i386 ca-certificates:i386 libarchive-cpio-perl
  krb5-locales:i386 libldap-common:i386 libgpm2:i386 publicsuffix:i386
  libsasl2-modules:i386 libtasn1-doc:i386 libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils-i686-linux-gnu
  bsdextrautils comerr-dev:i386 cpp-15-i686-linux-gnu cpp-i686-linux-gnu
  crossbuild-essential-i386 debhelper dh-autoreconf dh-strip-nondeterminism
  dwz fakeroot file g++-15-i686-linux-gnu g++-i686-linux-gnu gcc-15-base:i386
  gcc-15-cross-base gcc-15-i686-linux-gnu gcc-15-i686-linux-gnu-base
  gcc-i686-linux-gnu gettext gettext-base groff-base intltool-debian
  krb5-multidev:i386 libarchive-zip-perl libasan8:i386 libasan8-i386-cross
  libatomic1:i386 libatomic1-i386-cross libbamtools-dev:i386
  libbamtools2.5.3:i386 libbrotli-dev:i386 libbrotli1:i386 libbz2-1.0:i386
  libbz2-dev:i386 libc6:i386 libc6-dev:i386 libc6-dev-i386-cross
  libc6-i386-cross libcom-err2:i386 libcrypt-dev:i386 libcrypt1:i386
  libcurl3t64-gnutls:i386 libcurl4-gnutls-dev:i386 libdb5.3t64:i386
  libdebhelper-perl libdeflate-dev:i386 libdeflate0:i386 libelf1t64
  libevent-2.1-7t64:i386 libfakeroot libfastahack-dev:i386 libfastahack0:i386
  libffi8:i386 libfile-stripnondeterminism-perl libgcc-15-dev:i386
  libgcc-15-dev-i386-cross libgcc-s1:i386 libgcc-s1-i386-cross libgmp-dev:i386
  libgmp10:i386 libgmpxx4ldbl:i386 libgnutls-dane0t64:i386
  libgnutls-openssl27t64:i386 libgnutls28-dev:i386 libgnutls30t64:i386
  libgomp1:i386 libgomp1-i386-cross libgssapi-krb5-2:i386 libgssrpc4t64:i386
  libgzstream-dev:i386 libgzstream0:i386 libhogweed6t64:i386 libhts-dev:i386
  libhts3t64:i386 libhtscodecs2:i386 libidn2-0:i386 libidn2-dev:i386
  libitm1:i386 libitm1-i386-cross libk5crypto3:i386 libkadm5clnt-mit12:i386
  libkadm5srv-mit12:i386 libkdb5-10t64:i386 libkeyutils1:i386 libkrb5-3:i386
  libkrb5-dev:i386 libkrb5support0:i386 libldap-dev:i386 libldap2:i386
  liblzma-dev:i386 liblzma5:i386 libmagic-mgc libmagic1t64 libncurses6:i386
  libnettle8t64:i386 libnghttp2-14:i386 libnghttp2-dev:i386 libnghttp3-9:i386
  libnghttp3-dev:i386 libngtcp2-16:i386 libngtcp2-crypto-gnutls-dev:i386
  libngtcp2-crypto-gnutls8:i386 libngtcp2-dev:i386 libp11-kit-dev:i386
  libp11-kit0:i386 libpipeline1 libpkgconf3 libpsl-dev:i386 libpsl5t64:i386
  libquadmath0:i386 libquadmath0-i386-cross librtmp-dev:i386 librtmp1:i386
  libsasl2-2:i386 libsasl2-modules-db:i386 libsqlite3-0:i386
  libsqlite3-dev:i386 libssh2-1-dev:i386 libssh2-1t64:i386 libssl-dev:i386
  libssl3t64:i386 libstdc++-15-dev:i386 libstdc++-15-dev-i386-cross
  libstdc++6:i386 libstdc++6-i386-cross libtasn1-6:i386 libtasn1-6-dev:i386
  libtinfo6:i386 libtool libubsan1:i386 libubsan1-i386-cross libuchardet0
  libunbound8:i386 libunistring5 libunistring5:i386 libxml2-16
  libzstd-dev:i386 libzstd1:i386 linux-libc-dev-i386-cross m4 man-db
  nettle-dev:i386 pkgconf:i386 pkgconf-bin po-debconf samtools:i386
  sbuild-build-depends-main-dummy:i386 sensible-utils zlib1g:i386
  zlib1g-dev:i386
0 upgraded, 155 newly installed, 0 to remove and 0 not upgraded.
Need to get 119 MB of archives.
After this operation, 445 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [964 B]
Get:2 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.26 [27.0 kB]
Get:3 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-5 [338 kB]
Get:4 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-5 [103 kB]
Get:5 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.46-5 [43.7 kB]
Get:6 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.23.1-2+b1 [241 kB]
Get:7 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-2 [69.0 kB]
Get:8 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-9 [1130 kB]
Get:9 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.41.2-4 [97.3 kB]
Get:10 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB]
Get:11 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.13.1-1 [1453 kB]
Get:12 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.20-2 [315 kB]
Get:13 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.72-3.1 [494 kB]
Get:14 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20240727.1 [60.2 kB]
Get:15 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.18.1-2 [877 kB]
Get:16 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.23.1-2 [770 kB]
Get:17 http://mirror.einval.org/debian unstable/main i386 gcc-15-base i386 15.2.0-7 [53.3 kB]
Get:18 http://mirror.einval.org/debian unstable/main i386 libgcc-s1 i386 15.2.0-7 [87.0 kB]
Get:19 http://mirror.einval.org/debian unstable/main i386 libc6 i386 2.41-12 [2720 kB]
Get:20 http://mirror.einval.org/debian unstable/main i386 libcrypt1 i386 1:4.4.38-1 [95.7 kB]
Get:21 http://mirror.einval.org/debian unstable/main i386 libcrypt-dev i386 1:4.4.38-1 [126 kB]
Get:22 http://mirror.einval.org/debian unstable/main i386 libc6-dev i386 2.41-12 [1809 kB]
Get:23 http://mirror.einval.org/debian unstable/main i386 libcom-err2 i386 1.47.2-3+b3 [25.3 kB]
Get:24 http://mirror.einval.org/debian unstable/main i386 comerr-dev i386 2.1-1.47.2-3+b3 [57.1 kB]
Get:25 http://mirror.einval.org/debian unstable/main arm64 gcc-15-i686-linux-gnu-base arm64 15.2.0-7cross1 [53.5 kB]
Get:26 http://mirror.einval.org/debian unstable/main arm64 cpp-15-i686-linux-gnu arm64 15.2.0-7cross1 [11.3 MB]
Get:27 http://mirror.einval.org/debian unstable/main arm64 cpp-i686-linux-gnu arm64 4:15.2.0-4 [5288 B]
Get:28 http://mirror.einval.org/debian unstable/main arm64 binutils-i686-linux-gnu arm64 2.45-8 [1508 kB]
Get:29 http://mirror.einval.org/debian unstable/main arm64 gcc-15-cross-base all 15.2.0-7cross1 [48.9 kB]
Get:30 http://mirror.einval.org/debian unstable/main arm64 libc6-i386-cross all 2.41-11cross1 [1424 kB]
Get:31 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-i386-cross all 15.2.0-7cross1 [87.0 kB]
Get:32 http://mirror.einval.org/debian unstable/main arm64 libgomp1-i386-cross all 15.2.0-7cross1 [139 kB]
Get:33 http://mirror.einval.org/debian unstable/main arm64 libitm1-i386-cross all 15.2.0-7cross1 [27.5 kB]
Get:34 http://mirror.einval.org/debian unstable/main arm64 libatomic1-i386-cross all 15.2.0-7cross1 [7496 B]
Get:35 http://mirror.einval.org/debian unstable/main arm64 libasan8-i386-cross all 15.2.0-7cross1 [2642 kB]
Get:36 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-i386-cross all 15.2.0-7cross1 [734 kB]
Get:37 http://mirror.einval.org/debian unstable/main arm64 libubsan1-i386-cross all 15.2.0-7cross1 [1080 kB]
Get:38 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-i386-cross all 15.2.0-7cross1 [229 kB]
Get:39 http://mirror.einval.org/debian unstable/main arm64 libgcc-15-dev-i386-cross all 15.2.0-7cross1 [2621 kB]
Get:40 http://mirror.einval.org/debian unstable/main arm64 gcc-15-i686-linux-gnu arm64 15.2.0-7cross1 [21.8 MB]
Get:41 http://mirror.einval.org/debian unstable/main arm64 gcc-i686-linux-gnu arm64 4:15.2.0-4 [1444 B]
Get:42 http://mirror.einval.org/debian unstable/main arm64 linux-libc-dev-i386-cross all 6.12.38-1cross1 [2470 kB]
Get:43 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-i386-cross all 2.41-11cross1 [1806 kB]
Get:44 http://mirror.einval.org/debian unstable/main arm64 libstdc++-15-dev-i386-cross all 15.2.0-7cross1 [2489 kB]
Get:45 http://mirror.einval.org/debian unstable/main arm64 g++-15-i686-linux-gnu arm64 15.2.0-7cross1 [12.3 MB]
Get:46 http://mirror.einval.org/debian unstable/main arm64 g++-i686-linux-gnu arm64 4:15.2.0-4 [1192 B]
Get:47 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-i386 all 12.12 [3544 B]
Get:48 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.28 [92.4 kB]
Get:49 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.5.4-7 [540 kB]
Get:50 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 21 [12.2 kB]
Get:51 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:52 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB]
Get:53 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.15.0-1 [8812 B]
Get:54 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.194-1 [184 kB]
Get:55 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.16-2 [100 kB]
Get:56 http://mirror.einval.org/debian unstable/main arm64 libunistring5 arm64 1.3-2 [453 kB]
Get:57 http://mirror.einval.org/debian unstable/main arm64 libxml2-16 arm64 2.15.1+dfsg-0.3 [591 kB]
Get:58 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.23.1-2+b1 [1612 kB]
Get:59 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:60 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:61 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.28 [941 kB]
Get:62 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.37.1.2-1 [29.7 kB]
Get:63 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.37.1.2-1 [75.4 kB]
Get:64 http://mirror.einval.org/debian unstable/main i386 libkrb5support0 i386 1.21.3-5 [35.3 kB]
Get:65 http://mirror.einval.org/debian unstable/main i386 libk5crypto3 i386 1.21.3-5 [84.3 kB]
Get:66 http://mirror.einval.org/debian unstable/main i386 libkeyutils1 i386 1.6.3-6 [9964 B]
Get:67 http://mirror.einval.org/debian unstable/main i386 libzstd1 i386 1.5.7+dfsg-2 [308 kB]
Get:68 http://mirror.einval.org/debian unstable/main i386 zlib1g i386 1:1.3.dfsg+really1.3.1-1+b1 [84.7 kB]
Get:69 http://mirror.einval.org/debian unstable/main i386 libssl3t64 i386 3.5.4-1 [2417 kB]
Get:70 http://mirror.einval.org/debian unstable/main i386 libkrb5-3 i386 1.21.3-5 [355 kB]
Get:71 http://mirror.einval.org/debian unstable/main i386 libgssapi-krb5-2 i386 1.21.3-5 [149 kB]
Get:72 http://mirror.einval.org/debian unstable/main i386 libgssrpc4t64 i386 1.21.3-5 [63.6 kB]
Get:73 http://mirror.einval.org/debian unstable/main i386 libkadm5clnt-mit12 i386 1.21.3-5 [44.2 kB]
Get:74 http://mirror.einval.org/debian unstable/main i386 libkdb5-10t64 i386 1.21.3-5 [45.6 kB]
Get:75 http://mirror.einval.org/debian unstable/main i386 libkadm5srv-mit12 i386 1.21.3-5 [57.9 kB]
Get:76 http://mirror.einval.org/debian unstable/main i386 krb5-multidev i386 1.21.3-5 [126 kB]
Get:77 http://mirror.einval.org/debian unstable/main i386 libasan8 i386 15.2.0-7 [2651 kB]
Get:78 http://mirror.einval.org/debian unstable/main i386 libatomic1 i386 15.2.0-7 [7744 B]
Get:79 http://mirror.einval.org/debian unstable/main i386 libstdc++6 i386 15.2.0-7 [781 kB]
Get:80 http://mirror.einval.org/debian unstable/main i386 libbamtools2.5.3 i386 2.5.3+dfsg-1 [178 kB]
Get:81 http://mirror.einval.org/debian unstable/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB]
Get:82 http://mirror.einval.org/debian unstable/main i386 libbamtools-dev i386 2.5.3+dfsg-1 [241 kB]
Get:83 http://mirror.einval.org/debian unstable/main i386 libbrotli1 i386 1.1.0-2+b7 [299 kB]
Get:84 http://mirror.einval.org/debian unstable/main i386 libbrotli-dev i386 1.1.0-2+b7 [313 kB]
Get:85 http://mirror.einval.org/debian unstable/main i386 libbz2-1.0 i386 1.0.8-6 [38.1 kB]
Get:86 http://mirror.einval.org/debian unstable/main i386 libbz2-dev i386 1.0.8-6 [32.1 kB]
Get:87 http://mirror.einval.org/debian unstable/main i386 libnghttp3-9 i386 1.12.0-1 [80.1 kB]
Get:88 http://mirror.einval.org/debian unstable/main i386 libngtcp2-16 i386 1.16.0-1 [168 kB]
Get:89 http://mirror.einval.org/debian unstable/main i386 libgmp10 i386 2:6.3.0+dfsg-5 [572 kB]
Get:90 http://mirror.einval.org/debian unstable/main i386 libnettle8t64 i386 3.10.2-1 [318 kB]
Get:91 http://mirror.einval.org/debian unstable/main i386 libhogweed6t64 i386 3.10.2-1 [339 kB]
Get:92 http://mirror.einval.org/debian unstable/main i386 libunistring5 i386 1.3-2 [471 kB]
Get:93 http://mirror.einval.org/debian unstable/main i386 libidn2-0 i386 2.3.8-4 [111 kB]
Get:94 http://mirror.einval.org/debian unstable/main i386 libffi8 i386 3.5.2-2 [21.8 kB]
Get:95 http://mirror.einval.org/debian unstable/main i386 libp11-kit0 i386 0.25.9-2 [435 kB]
Get:96 http://mirror.einval.org/debian unstable/main i386 libtasn1-6 i386 4.20.0-2 [51.6 kB]
Get:97 http://mirror.einval.org/debian unstable/main i386 libgnutls30t64 i386 3.8.10-3 [1485 kB]
Get:98 http://mirror.einval.org/debian unstable/main i386 libdb5.3t64 i386 5.3.28+dfsg2-10 [767 kB]
Get:99 http://mirror.einval.org/debian unstable/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-10 [20.8 kB]
Get:100 http://mirror.einval.org/debian unstable/main i386 libsasl2-2 i386 2.1.28+dfsg1-10 [61.4 kB]
Get:101 http://mirror.einval.org/debian unstable/main i386 libldap2 i386 2.6.10+dfsg-1 [208 kB]
Get:102 http://mirror.einval.org/debian unstable/main i386 libnghttp2-14 i386 1.64.0-1.1+b1 [84.0 kB]
Get:103 http://mirror.einval.org/debian unstable/main i386 libngtcp2-crypto-gnutls8 i386 1.16.0-1 [25.6 kB]
Get:104 http://mirror.einval.org/debian unstable/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB]
Get:105 http://mirror.einval.org/debian unstable/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-3 [61.9 kB]
Get:106 http://mirror.einval.org/debian unstable/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB]
Get:107 http://mirror.einval.org/debian unstable/main i386 libcurl3t64-gnutls i386 8.17.0-1 [446 kB]
Get:108 http://mirror.einval.org/debian unstable/main i386 libevent-2.1-7t64 i386 2.1.12-stable-10+b1 [195 kB]
Get:109 http://mirror.einval.org/debian unstable/main i386 libunbound8 i386 1.24.1-2 [648 kB]
Get:110 http://mirror.einval.org/debian unstable/main i386 libgnutls-dane0t64 i386 3.8.10-3 [456 kB]
Get:111 http://mirror.einval.org/debian unstable/main i386 libgnutls-openssl27t64 i386 3.8.10-3 [455 kB]
Get:112 http://mirror.einval.org/debian unstable/main i386 libidn2-dev i386 2.3.8-4 [105 kB]
Get:113 http://mirror.einval.org/debian unstable/main i386 libp11-kit-dev i386 0.25.9-2 [220 kB]
Get:114 http://mirror.einval.org/debian unstable/main i386 libtasn1-6-dev i386 4.20.0-2 [103 kB]
Get:115 http://mirror.einval.org/debian unstable/main i386 libgmpxx4ldbl i386 2:6.3.0+dfsg-5 [330 kB]
Get:116 http://mirror.einval.org/debian unstable/main i386 libgmp-dev i386 2:6.3.0+dfsg-5 [661 kB]
Get:117 http://mirror.einval.org/debian unstable/main i386 nettle-dev i386 3.10.2-1 [1338 kB]
Get:118 http://mirror.einval.org/debian unstable/main i386 libgnutls28-dev i386 3.8.10-3 [1487 kB]
Get:119 http://mirror.einval.org/debian unstable/main i386 libkrb5-dev i386 1.21.3-5 [16.1 kB]
Get:120 http://mirror.einval.org/debian unstable/main i386 libldap-dev i386 2.6.10+dfsg-1 [333 kB]
Get:121 http://mirror.einval.org/debian unstable/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get:122 http://mirror.einval.org/debian unstable/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get:123 http://mirror.einval.org/debian unstable/main i386 pkgconf i386 1.8.1-4 [26.2 kB]
Get:124 http://mirror.einval.org/debian unstable/main i386 libnghttp2-dev i386 1.64.0-1.1+b1 [125 kB]
Get:125 http://mirror.einval.org/debian unstable/main i386 libnghttp3-dev i386 1.12.0-1 [109 kB]
Get:126 http://mirror.einval.org/debian unstable/main i386 libngtcp2-crypto-gnutls-dev i386 1.16.0-1 [25.9 kB]
Get:127 http://mirror.einval.org/debian unstable/main i386 libngtcp2-dev i386 1.16.0-1 [229 kB]
Get:128 http://mirror.einval.org/debian unstable/main i386 libpsl-dev i386 0.21.2-1.1+b1 [78.4 kB]
Get:129 http://mirror.einval.org/debian unstable/main i386 librtmp-dev i386 2.4+20151223.gitfa8646d.1-3 [72.2 kB]
Get:130 http://mirror.einval.org/debian unstable/main i386 libssl-dev i386 3.5.4-1 [3011 kB]
Get:131 http://mirror.einval.org/debian unstable/main i386 libssh2-1-dev i386 1.11.1-1 [407 kB]
Get:132 http://mirror.einval.org/debian unstable/main i386 libzstd-dev i386 1.5.7+dfsg-2 [375 kB]
Get:133 http://mirror.einval.org/debian unstable/main i386 libcurl4-gnutls-dev i386 8.17.0-1 [584 kB]
Get:134 http://mirror.einval.org/debian unstable/main i386 libdeflate0 i386 1.23-2 [48.2 kB]
Get:135 http://mirror.einval.org/debian unstable/main i386 libdeflate-dev i386 1.23-2 [57.3 kB]
Get:136 http://mirror.einval.org/debian unstable/main i386 libfastahack0 i386 1.0.0+dfsg-11+b2 [27.4 kB]
Get:137 http://mirror.einval.org/debian unstable/main i386 libfastahack-dev i386 1.0.0+dfsg-11+b2 [29.5 kB]
Get:138 http://mirror.einval.org/debian unstable/main i386 libgomp1 i386 15.2.0-7 [142 kB]
Get:139 http://mirror.einval.org/debian unstable/main i386 libitm1 i386 15.2.0-7 [28.0 kB]
Get:140 http://mirror.einval.org/debian unstable/main i386 libubsan1 i386 15.2.0-7 [1081 kB]
Get:141 http://mirror.einval.org/debian unstable/main i386 libquadmath0 i386 15.2.0-7 [229 kB]
Get:142 http://mirror.einval.org/debian unstable/main i386 libgcc-15-dev i386 15.2.0-7 [2625 kB]
Get:143 http://mirror.einval.org/debian unstable/main i386 libgzstream0 i386 1.5+git20171107.9a20658-3 [7192 B]
Get:144 http://mirror.einval.org/debian unstable/main i386 libgzstream-dev i386 1.5+git20171107.9a20658-3 [7568 B]
Get:145 http://mirror.einval.org/debian unstable/main i386 libhtscodecs2 i386 1.6.1-2 [70.9 kB]
Get:146 http://mirror.einval.org/debian unstable/main i386 liblzma5 i386 5.8.1-2 [320 kB]
Get:147 http://mirror.einval.org/debian unstable/main i386 libhts3t64 i386 1.22.1+ds2-1 [516 kB]
Get:148 http://mirror.einval.org/debian unstable/main i386 liblzma-dev i386 5.8.1-2 [363 kB]
Get:149 http://mirror.einval.org/debian unstable/main i386 libhts-dev i386 1.22.1+ds2-1 [1770 kB]
Get:150 http://mirror.einval.org/debian unstable/main i386 libtinfo6 i386 6.5+20250216-2 [350 kB]
Get:151 http://mirror.einval.org/debian unstable/main i386 libncurses6 i386 6.5+20250216-2 [112 kB]
Get:152 http://mirror.einval.org/debian unstable/main i386 libsqlite3-0 i386 3.46.1-8 [992 kB]
Get:153 http://mirror.einval.org/debian unstable/main i386 libsqlite3-dev i386 3.46.1-8 [1198 kB]
Get:154 http://mirror.einval.org/debian unstable/main i386 libstdc++-15-dev i386 15.2.0-7 [2507 kB]
Get:155 http://mirror.einval.org/debian unstable/main i386 samtools i386 1.22.1-1 [730 kB]
Preconfiguring packages ...
Fetched 119 MB in 2s (69.1 MB/s)
Selecting previously unselected package sensible-utils.
(Reading database ... 12024 files and directories currently installed.)
Preparing to unpack .../000-sensible-utils_0.0.26_all.deb ...
Unpacking sensible-utils (0.0.26) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../001-libmagic-mgc_1%3a5.46-5_arm64.deb ...
Unpacking libmagic-mgc (1:5.46-5) ...
Selecting previously unselected package libmagic1t64:arm64.
Preparing to unpack .../002-libmagic1t64_1%3a5.46-5_arm64.deb ...
Unpacking libmagic1t64:arm64 (1:5.46-5) ...
Selecting previously unselected package file.
Preparing to unpack .../003-file_1%3a5.46-5_arm64.deb ...
Unpacking file (1:5.46-5) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../004-gettext-base_0.23.1-2+b1_arm64.deb ...
Unpacking gettext-base (0.23.1-2+b1) ...
Selecting previously unselected package libuchardet0:arm64.
Preparing to unpack .../005-libuchardet0_0.0.8-2_arm64.deb ...
Unpacking libuchardet0:arm64 (0.0.8-2) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../006-groff-base_1.23.0-9_arm64.deb ...
Unpacking groff-base (1.23.0-9) ...
Selecting previously unselected package bsdextrautils.
Preparing to unpack .../007-bsdextrautils_2.41.2-4_arm64.deb ...
Unpacking bsdextrautils (2.41.2-4) ...
Selecting previously unselected package libpipeline1:arm64.
Preparing to unpack .../008-libpipeline1_1.5.8-1_arm64.deb ...
Unpacking libpipeline1:arm64 (1.5.8-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../009-man-db_2.13.1-1_arm64.deb ...
Unpacking man-db (2.13.1-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../010-m4_1.4.20-2_arm64.deb ...
Unpacking m4 (1.4.20-2) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../011-autoconf_2.72-3.1_all.deb ...
Unpacking autoconf (2.72-3.1) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../012-autotools-dev_20240727.1_all.deb ...
Unpacking autotools-dev (20240727.1) ...
Selecting previously unselected package automake.
Preparing to unpack .../013-automake_1%3a1.18.1-2_all.deb ...
Unpacking automake (1:1.18.1-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../014-autopoint_0.23.1-2_all.deb ...
Unpacking autopoint (0.23.1-2) ...
Selecting previously unselected package gcc-15-base:i386.
Preparing to unpack .../015-gcc-15-base_15.2.0-7_i386.deb ...
Unpacking gcc-15-base:i386 (15.2.0-7) ...
Selecting previously unselected package libgcc-s1:i386.
Preparing to unpack .../016-libgcc-s1_15.2.0-7_i386.deb ...
Unpacking libgcc-s1:i386 (15.2.0-7) ...
Selecting previously unselected package libc6:i386.
Preparing to unpack .../017-libc6_2.41-12_i386.deb ...
Unpacking libc6:i386 (2.41-12) ...
Selecting previously unselected package libcrypt1:i386.
Preparing to unpack .../018-libcrypt1_1%3a4.4.38-1_i386.deb ...
Unpacking libcrypt1:i386 (1:4.4.38-1) ...
Selecting previously unselected package libcrypt-dev:i386.
Preparing to unpack .../019-libcrypt-dev_1%3a4.4.38-1_i386.deb ...
Unpacking libcrypt-dev:i386 (1:4.4.38-1) ...
Selecting previously unselected package libc6-dev:i386.
Preparing to unpack .../020-libc6-dev_2.41-12_i386.deb ...
Unpacking libc6-dev:i386 (2.41-12) ...
Selecting previously unselected package libcom-err2:i386.
Preparing to unpack .../021-libcom-err2_1.47.2-3+b3_i386.deb ...
Unpacking libcom-err2:i386 (1.47.2-3+b3) ...
Selecting previously unselected package comerr-dev:i386.
Preparing to unpack .../022-comerr-dev_2.1-1.47.2-3+b3_i386.deb ...
Unpacking comerr-dev:i386 (2.1-1.47.2-3+b3) ...
Selecting previously unselected package gcc-15-i686-linux-gnu-base:arm64.
Preparing to unpack .../023-gcc-15-i686-linux-gnu-base_15.2.0-7cross1_arm64.deb ...
Unpacking gcc-15-i686-linux-gnu-base:arm64 (15.2.0-7cross1) ...
Selecting previously unselected package cpp-15-i686-linux-gnu.
Preparing to unpack .../024-cpp-15-i686-linux-gnu_15.2.0-7cross1_arm64.deb ...
Unpacking cpp-15-i686-linux-gnu (15.2.0-7cross1) ...
Selecting previously unselected package cpp-i686-linux-gnu.
Preparing to unpack .../025-cpp-i686-linux-gnu_4%3a15.2.0-4_arm64.deb ...
Unpacking cpp-i686-linux-gnu (4:15.2.0-4) ...
Selecting previously unselected package binutils-i686-linux-gnu.
Preparing to unpack .../026-binutils-i686-linux-gnu_2.45-8_arm64.deb ...
Unpacking binutils-i686-linux-gnu (2.45-8) ...
Selecting previously unselected package gcc-15-cross-base.
Preparing to unpack .../027-gcc-15-cross-base_15.2.0-7cross1_all.deb ...
Unpacking gcc-15-cross-base (15.2.0-7cross1) ...
Selecting previously unselected package libc6-i386-cross.
Preparing to unpack .../028-libc6-i386-cross_2.41-11cross1_all.deb ...
Unpacking libc6-i386-cross (2.41-11cross1) ...
Selecting previously unselected package libgcc-s1-i386-cross.
Preparing to unpack .../029-libgcc-s1-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libgcc-s1-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package libgomp1-i386-cross.
Preparing to unpack .../030-libgomp1-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libgomp1-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package libitm1-i386-cross.
Preparing to unpack .../031-libitm1-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libitm1-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package libatomic1-i386-cross.
Preparing to unpack .../032-libatomic1-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libatomic1-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package libasan8-i386-cross.
Preparing to unpack .../033-libasan8-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libasan8-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package libstdc++6-i386-cross.
Preparing to unpack .../034-libstdc++6-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libstdc++6-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package libubsan1-i386-cross.
Preparing to unpack .../035-libubsan1-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libubsan1-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package libquadmath0-i386-cross.
Preparing to unpack .../036-libquadmath0-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libquadmath0-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package libgcc-15-dev-i386-cross.
Preparing to unpack .../037-libgcc-15-dev-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libgcc-15-dev-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package gcc-15-i686-linux-gnu.
Preparing to unpack .../038-gcc-15-i686-linux-gnu_15.2.0-7cross1_arm64.deb ...
Unpacking gcc-15-i686-linux-gnu (15.2.0-7cross1) ...
Selecting previously unselected package gcc-i686-linux-gnu.
Preparing to unpack .../039-gcc-i686-linux-gnu_4%3a15.2.0-4_arm64.deb ...
Unpacking gcc-i686-linux-gnu (4:15.2.0-4) ...
Selecting previously unselected package linux-libc-dev-i386-cross.
Preparing to unpack .../040-linux-libc-dev-i386-cross_6.12.38-1cross1_all.deb ...
Unpacking linux-libc-dev-i386-cross (6.12.38-1cross1) ...
Selecting previously unselected package libc6-dev-i386-cross.
Preparing to unpack .../041-libc6-dev-i386-cross_2.41-11cross1_all.deb ...
Unpacking libc6-dev-i386-cross (2.41-11cross1) ...
Selecting previously unselected package libstdc++-15-dev-i386-cross.
Preparing to unpack .../042-libstdc++-15-dev-i386-cross_15.2.0-7cross1_all.deb ...
Unpacking libstdc++-15-dev-i386-cross (15.2.0-7cross1) ...
Selecting previously unselected package g++-15-i686-linux-gnu.
Preparing to unpack .../043-g++-15-i686-linux-gnu_15.2.0-7cross1_arm64.deb ...
Unpacking g++-15-i686-linux-gnu (15.2.0-7cross1) ...
Selecting previously unselected package g++-i686-linux-gnu.
Preparing to unpack .../044-g++-i686-linux-gnu_4%3a15.2.0-4_arm64.deb ...
Unpacking g++-i686-linux-gnu (4:15.2.0-4) ...
Selecting previously unselected package crossbuild-essential-i386.
Preparing to unpack .../045-crossbuild-essential-i386_12.12_all.deb ...
Unpacking crossbuild-essential-i386 (12.12) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../046-libdebhelper-perl_13.28_all.deb ...
Unpacking libdebhelper-perl (13.28) ...
Selecting previously unselected package libtool.
Preparing to unpack .../047-libtool_2.5.4-7_all.deb ...
Unpacking libtool (2.5.4-7) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../048-dh-autoreconf_21_all.deb ...
Unpacking dh-autoreconf (21) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../049-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../050-libfile-stripnondeterminism-perl_1.15.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.15.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../051-dh-strip-nondeterminism_1.15.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.15.0-1) ...
Selecting previously unselected package libelf1t64:arm64.
Preparing to unpack .../052-libelf1t64_0.194-1_arm64.deb ...
Unpacking libelf1t64:arm64 (0.194-1) ...
Selecting previously unselected package dwz.
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Unpacking dwz (0.16-2) ...
Selecting previously unselected package libunistring5:arm64.
Preparing to unpack .../054-libunistring5_1.3-2_arm64.deb ...
Unpacking libunistring5:arm64 (1.3-2) ...
Selecting previously unselected package libxml2-16:arm64.
Preparing to unpack .../055-libxml2-16_2.15.1+dfsg-0.3_arm64.deb ...
Unpacking libxml2-16:arm64 (2.15.1+dfsg-0.3) ...
Selecting previously unselected package gettext.
Preparing to unpack .../056-gettext_0.23.1-2+b1_arm64.deb ...
Unpacking gettext (0.23.1-2+b1) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../057-intltool-debian_0.35.0+20060710.6_all.deb ...
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Setting up pkgconf:i386 (1.8.1-4) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up libgcc-s1-i386-cross (15.2.0-7cross1) ...
Setting up dh-autoreconf (21) ...
Setting up libitm1-i386-cross (15.2.0-7cross1) ...
Setting up dh-strip-nondeterminism (1.15.0-1) ...
Setting up groff-base (1.23.0-9) ...
Setting up cpp-i686-linux-gnu (4:15.2.0-4) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.13.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libasan8-i386-cross (15.2.0-7cross1) ...
Setting up libstdc++6-i386-cross (15.2.0-7cross1) ...
Setting up debhelper (13.28) ...
Setting up libubsan1-i386-cross (15.2.0-7cross1) ...
Setting up libgcc-15-dev-i386-cross (15.2.0-7cross1) ...
Setting up libstdc++-15-dev-i386-cross (15.2.0-7cross1) ...
Setting up gcc-15-i686-linux-gnu (15.2.0-7cross1) ...
Setting up g++-15-i686-linux-gnu (15.2.0-7cross1) ...
Setting up gcc-i686-linux-gnu (4:15.2.0-4) ...
Setting up g++-i686-linux-gnu (4:15.2.0-4) ...
Setting up crossbuild-essential-i386 (12.12) ...
Setting up libgcc-s1:i386 (15.2.0-7) ...
Setting up libc6:i386 (2.41-12) ...
Setting up libnghttp3-9:i386 (1.12.0-1) ...
Setting up libnghttp3-dev:i386 (1.12.0-1) ...
Setting up libdb5.3t64:i386 (5.3.28+dfsg2-10) ...
Setting up libffi8:i386 (3.5.2-2) ...
Setting up libasan8:i386 (15.2.0-7) ...
Setting up libtasn1-6:i386 (4.20.0-2) ...
Setting up libngtcp2-16:i386 (1.16.0-1) ...
Setting up libbz2-1.0:i386 (1.0.8-6) ...
Setting up libtasn1-6-dev:i386 (4.20.0-2) ...
Setting up libstdc++6:i386 (15.2.0-7) ...
Setting up libitm1:i386 (15.2.0-7) ...
Setting up libtinfo6:i386 (6.5+20250216-2) ...
Setting up libhtscodecs2:i386 (1.6.1-2) ...
Setting up libzstd1:i386 (1.5.7+dfsg-2) ...
Setting up libkeyutils1:i386 (1.6.3-6) ...
Setting up libzstd-dev:i386 (1.5.7+dfsg-2) ...
Setting up liblzma5:i386 (5.8.1-2) ...
Setting up libbrotli1:i386 (1.1.0-2+b7) ...
Setting up libsqlite3-0:i386 (3.46.1-8) ...
Setting up libnghttp2-14:i386 (1.64.0-1.1+b1) ...
Setting up libdeflate0:i386 (1.23-2) ...
Setting up libevent-2.1-7t64:i386 (2.1.12-stable-10+b1) ...
Setting up zlib1g:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libcrypt1:i386 (1:4.4.38-1) ...
Setting up libcom-err2:i386 (1.47.2-3+b3) ...
Setting up libngtcp2-dev:i386 (1.16.0-1) ...
Setting up libgomp1:i386 (15.2.0-7) ...
Setting up libfastahack0:i386 (1.0.0+dfsg-11+b2) ...
Setting up libkrb5support0:i386 (1.21.3-5) ...
Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-10) ...
Setting up libfastahack-dev:i386 (1.0.0+dfsg-11+b2) ...
Setting up libnettle8t64:i386 (3.10.2-1) ...
Setting up libgmp10:i386 (2:6.3.0+dfsg-5) ...
Setting up libncurses6:i386 (6.5+20250216-2) ...
Setting up libquadmath0:i386 (15.2.0-7) ...
Setting up libp11-kit0:i386 (0.25.9-2) ...
Setting up libunistring5:i386 (1.3-2) ...
Setting up libatomic1:i386 (15.2.0-7) ...
Setting up libk5crypto3:i386 (1.21.3-5) ...
Setting up libgzstream0:i386 (1.5+git20171107.9a20658-3) ...
Setting up liblzma-dev:i386 (5.8.1-2) ...
Setting up libubsan1:i386 (15.2.0-7) ...
Setting up libbamtools2.5.3:i386 (2.5.3+dfsg-1) ...
Setting up libhogweed6t64:i386 (3.10.2-1) ...
Setting up libcrypt-dev:i386 (1:4.4.38-1) ...
Setting up libc6-dev:i386 (2.41-12) ...
Setting up libdeflate-dev:i386 (1.23-2) ...
Setting up libbrotli-dev:i386 (1.1.0-2+b7) ...
Setting up libp11-kit-dev:i386 (0.25.9-2) ...
Setting up libbz2-dev:i386 (1.0.8-6) ...
Setting up libnghttp2-dev:i386 (1.64.0-1.1+b1) ...
Setting up libgcc-15-dev:i386 (15.2.0-7) ...
Setting up libssl3t64:i386 (3.5.4-1) ...
Setting up libidn2-0:i386 (2.3.8-4) ...
Setting up libgzstream-dev:i386 (1.5+git20171107.9a20658-3) ...
Setting up libunbound8:i386 (1.24.1-2) ...
Setting up libgmpxx4ldbl:i386 (2:6.3.0+dfsg-5) ...
Setting up libstdc++-15-dev:i386 (15.2.0-7) ...
Setting up libsqlite3-dev:i386 (3.46.1-8) ...
Setting up comerr-dev:i386 (2.1-1.47.2-3+b3) ...
Setting up libssl-dev:i386 (3.5.4-1) ...
Setting up libidn2-dev:i386 (2.3.8-4) ...
Setting up libsasl2-2:i386 (2.1.28+dfsg1-10) ...
Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libkrb5-3:i386 (1.21.3-5) ...
Setting up libssh2-1t64:i386 (1.11.1-1) ...
Setting up libldap2:i386 (2.6.10+dfsg-1) ...
Setting up libgnutls30t64:i386 (3.8.10-3) ...
Setting up libgnutls-openssl27t64:i386 (3.8.10-3) ...
Setting up libgmp-dev:i386 (2:6.3.0+dfsg-5) ...
Setting up nettle-dev:i386 (3.10.2-1) ...
Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ...
Setting up libpsl-dev:i386 (0.21.2-1.1+b1) ...
Setting up libgnutls-dane0t64:i386 (3.8.10-3) ...
Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-3) ...
Setting up libldap-dev:i386 (2.6.10+dfsg-1) ...
Setting up libbamtools-dev:i386 (2.5.3+dfsg-1) ...
Setting up libgssapi-krb5-2:i386 (1.21.3-5) ...
Setting up libssh2-1-dev:i386 (1.11.1-1) ...
Setting up libngtcp2-crypto-gnutls8:i386 (1.16.0-1) ...
Setting up libgnutls28-dev:i386 (3.8.10-3) ...
Setting up libcurl3t64-gnutls:i386 (8.17.0-1) ...
Setting up libngtcp2-crypto-gnutls-dev:i386 (1.16.0-1) ...
Setting up libgssrpc4t64:i386 (1.21.3-5) ...
Setting up librtmp-dev:i386 (2.4+20151223.gitfa8646d.1-3) ...
Setting up libhts3t64:i386 (1.22.1+ds2-1) ...
Setting up libkadm5clnt-mit12:i386 (1.21.3-5) ...
Setting up libkdb5-10t64:i386 (1.21.3-5) ...
Setting up samtools:i386 (1.22.1-1) ...
Setting up libkadm5srv-mit12:i386 (1.21.3-5) ...
Setting up krb5-multidev:i386 (1.21.3-5) ...
Setting up libkrb5-dev:i386 (1.21.3-5) ...
Setting up libcurl4-gnutls-dev:i386 (8.17.0-1) ...
Setting up libhts-dev:i386 (1.22.1+ds2-1) ...
Setting up sbuild-build-depends-main-dummy:i386 (0.invalid.0) ...
Processing triggers for libc-bin (2.41-12) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (i386 included in any all)

+------------------------------------------------------------------------------+
| Build environment                                                            |
+------------------------------------------------------------------------------+

Kernel: Linux 6.1.0-37-arm64 #1 SMP Debian 6.1.140-1 (2025-05-22) arm64 (aarch64)
Toolchain package versions: binutils_2.45-8 dpkg-dev_1.22.21 g++-15_15.2.0-7 gcc-15_15.2.0-7 libc6-dev_2.41-12 libstdc++-15-dev_15.2.0-7 libstdc++-15-dev-i386-cross_15.2.0-7cross1 libstdc++6_15.2.0-7 libstdc++6-i386-cross_15.2.0-7cross1 linux-libc-dev_6.17.7-1
Package versions: apt_3.1.11 apt-utils_3.1.11 autoconf_2.72-3.1 automake_1:1.18.1-2 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.8 bash_5.3-1 binutils_2.45-8 binutils-aarch64-linux-gnu_2.45-8 binutils-common_2.45-8 binutils-i686-linux-gnu_2.45-8 bsdextrautils_2.41.2-4 build-essential_12.12 bzip2_1.0.8-6 comerr-dev_2.1-1.47.2-3+b3 coreutils_9.7-3 cpp_4:15.2.0-4 cpp-15_15.2.0-7 cpp-15-aarch64-linux-gnu_15.2.0-7 cpp-15-i686-linux-gnu_15.2.0-7cross1 cpp-aarch64-linux-gnu_4:15.2.0-4 cpp-i686-linux-gnu_4:15.2.0-4 crossbuild-essential-i386_12.12 dash_0.5.12-12 debconf_1.5.91 debhelper_13.28 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_21 dh-strip-nondeterminism_1.15.0-1 diffutils_1:3.12-1 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.16-2 fakeroot_1.37.1.2-1 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-4 g++-15_15.2.0-7 g++-15-aarch64-linux-gnu_15.2.0-7 g++-15-i686-linux-gnu_15.2.0-7cross1 g++-aarch64-linux-gnu_4:15.2.0-4 g++-i686-linux-gnu_4:15.2.0-4 gcc_4:15.2.0-4 gcc-15_15.2.0-7 gcc-15-aarch64-linux-gnu_15.2.0-7 gcc-15-base_15.2.0-7 gcc-15-cross-base_15.2.0-7cross1 gcc-15-i686-linux-gnu_15.2.0-7cross1 gcc-15-i686-linux-gnu-base_15.2.0-7cross1 gcc-aarch64-linux-gnu_4:15.2.0-4 gcc-i686-linux-gnu_4:15.2.0-4 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 grep_3.12-1 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 krb5-multidev_1.21.3-5 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.11 libarchive-zip-perl_1.68-1 libasan8_15.2.0-7 libasan8-i386-cross_15.2.0-7cross1 libatomic1_15.2.0-7 libatomic1-i386-cross_15.2.0-7cross1 libattr1_1:2.5.2-3 libaudit-common_1:4.1.2-1 libaudit1_1:4.1.2-1 libbamtools-dev_2.5.3+dfsg-1 libbamtools2.5.3_2.5.3+dfsg-1 libbinutils_2.45-8 libblkid1_2.41.2-4 libbrotli-dev_1.1.0-2+b7 libbrotli1_1.1.0-2+b7 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libc6-dev-i386-cross_2.41-11cross1 libc6-i386-cross_2.41-11cross1 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-7 libcom-err2_1.47.2-3+b3 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-8 libctf0_2.45-8 libcurl3t64-gnutls_8.17.0-1 libcurl4-gnutls-dev_8.17.0-1 libdb5.3t64_5.3.28+dfsg2-10 libdebconfclient0_0.280 libdebhelper-perl_13.28 libdeflate-dev_1.23-2 libdeflate0_1.23-2 libdpkg-perl_1.22.21 libelf1t64_0.194-1 libevent-2.1-7t64_2.1.12-stable-10+b1 libfakeroot_1.37.1.2-1 libfastahack-dev_1.0.0+dfsg-11+b2 libfastahack0_1.0.0+dfsg-11+b2 libffi8_3.5.2-2 libfile-stripnondeterminism-perl_1.15.0-1 libgcc-15-dev_15.2.0-7 libgcc-15-dev-i386-cross_15.2.0-7cross1 libgcc-s1_15.2.0-7 libgcc-s1-i386-cross_15.2.0-7cross1 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgmp-dev_2:6.3.0+dfsg-5 libgmp10_2:6.3.0+dfsg-5 libgmpxx4ldbl_2:6.3.0+dfsg-5 libgnutls-dane0t64_3.8.10-3 libgnutls-openssl27t64_3.8.10-3 libgnutls28-dev_3.8.10-3 libgnutls30t64_3.8.10-3 libgomp1_15.2.0-7 libgomp1-i386-cross_15.2.0-7cross1 libgprofng0_2.45-8 libgssapi-krb5-2_1.21.3-5 libgssrpc4t64_1.21.3-5 libgzstream-dev_1.5+git20171107.9a20658-3 libgzstream0_1.5+git20171107.9a20658-3 libhogweed6t64_3.10.2-1 libhts-dev_1.22.1+ds2-1 libhts3t64_1.22.1+ds2-1 libhtscodecs2_1.6.1-2 libhwasan0_15.2.0-7 libidn2-0_2.3.8-4 libidn2-dev_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-7 libitm1-i386-cross_15.2.0-7cross1 libjansson4_2.14-2+b3 libk5crypto3_1.21.3-5 libkadm5clnt-mit12_1.21.3-5 libkadm5srv-mit12_1.21.3-5 libkdb5-10t64_1.21.3-5 libkeyutils1_1.6.3-6 libkrb5-3_1.21.3-5 libkrb5-dev_1.21.3-5 libkrb5support0_1.21.3-5 libldap-dev_2.6.10+dfsg-1 libldap2_2.6.10+dfsg-1 liblsan0_15.2.0-7 liblz4-1_1.10.0-6 liblzma-dev_5.8.1-2 liblzma5_5.8.1-2 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.2-4 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libncurses6_6.5+20250216-2 libnettle8t64_3.10.2-1 libnghttp2-14_1.64.0-1.1+b1 libnghttp2-dev_1.64.0-1.1+b1 libnghttp3-9_1.12.0-1 libnghttp3-dev_1.12.0-1 libngtcp2-16_1.16.0-1 libngtcp2-crypto-gnutls-dev_1.16.0-1 libngtcp2-crypto-gnutls8_1.16.0-1 libngtcp2-dev_1.16.0-1 libp11-kit-dev_0.25.9-2 libp11-kit0_0.25.9-2 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.46-1 libperl5.40_5.40.1-6 libpipeline1_1.5.8-1 libpkgconf3_1.8.1-4 libpsl-dev_0.21.2-1.1+b1 libpsl5t64_0.21.2-1.1+b1 libquadmath0_15.2.0-7 libquadmath0-i386-cross_15.2.0-7cross1 librtmp-dev_2.4+20151223.gitfa8646d.1-3 librtmp1_2.4+20151223.gitfa8646d.1-3 libsasl2-2_2.1.28+dfsg1-10 libsasl2-modules-db_2.1.28+dfsg1-10 libseccomp2_2.6.0-2 libselinux1_3.9-2 libsframe2_2.45-8 libsmartcols1_2.41.2-4 libsqlite3-0_3.46.1-8 libsqlite3-dev_3.46.1-8 libssh2-1-dev_1.11.1-1 libssh2-1t64_1.11.1-1 libssl-dev_3.5.4-1 libssl3t64_3.5.4-1 libstdc++-15-dev_15.2.0-7 libstdc++-15-dev-i386-cross_15.2.0-7cross1 libstdc++6_15.2.0-7 libstdc++6-i386-cross_15.2.0-7cross1 libsystemd0_258.1-2 libtasn1-6_4.20.0-2 libtasn1-6-dev_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-7 libtsan2_15.2.0-7 libubsan1_15.2.0-7 libubsan1-i386-cross_15.2.0-7cross1 libuchardet0_0.0.8-2 libudev1_258.1-2 libunbound8_1.24.1-2 libunistring5_1.3-2 libuuid1_2.41.2-4 libxml2-16_2.15.1+dfsg-0.3 libxxhash0_0.8.3-2 libzstd-dev_1.5.7+dfsg-2 libzstd1_1.5.7+dfsg-2 linux-libc-dev_6.17.7-1 linux-libc-dev-i386-cross_6.12.38-1cross1 login_1:4.16.0-2+really2.41.2-4 login.defs_1:4.18.0-2 m4_1.4.20-2 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 nettle-dev_3.10.2-1 openssl-provider-legacy_3.5.4-1 patch_2.8-2 perl_5.40.1-6 perl-base_5.40.1-6 perl-modules-5.40_5.40.1-6 pkgconf_1.8.1-4 pkgconf-bin_1.8.1-4 po-debconf_1.0.21+nmu1 rpcsvc-proto_1.4.3-1+b1 samtools_1.22.1-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2+b1 sensible-utils_0.0.26 sqv_1.3.0-3 sysvinit-utils_3.15-5 tar_1.35+dfsg-3.1 util-linux_2.41.2-4 xz-utils_5.8.1-2 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1

+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


Unpack source
-------------

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512

Format: 3.0 (quilt)
Source: lumpy-sv
Binary: lumpy-sv, lumpy-sv-examples
Architecture: any all
Version: 0.3.1+dfsg-8
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://github.com/arq5x/lumpy-sv
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/lumpy-sv
Vcs-Git: https://salsa.debian.org/med-team/lumpy-sv.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), libbamtools-dev, libfastahack-dev, libgzstream-dev, libsqlite3-dev, libhts-dev, libssl-dev, libcurl4-gnutls-dev, samtools
Package-List:
 lumpy-sv deb science optional arch=any
 lumpy-sv-examples deb science optional arch=all
Checksums-Sha1:
 b75a3ba46fb5197a96d8d5dccda356384c06bb77 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz
 4237faac649ff49f71fa9edac73689768ab3ad27 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz
Checksums-Sha256:
 78a6fe414739286d1f799bbdf3e34b9a1d6ed03b4c6dd17bfef1fcbba84bd35a 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz
 10a8ee20f04d1255322f09643940238685468d0f10e21cae7a046e834f2a4798 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz
Files:
 1167e4a94bceb29ac5b83cb170058e25 111836 lumpy-sv_0.3.1+dfsg.orig.tar.xz
 5876c8eaebf4fc93883197da876153eb 39265332 lumpy-sv_0.3.1+dfsg-8.debian.tar.xz

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dpkg-source: warning: cannot verify inline signature for ./lumpy-sv_0.3.1+dfsg-8.dsc: no acceptable signature found
dpkg-source: info: extracting lumpy-sv in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking lumpy-sv_0.3.1+dfsg-8.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libs.patch
dpkg-source: info: applying lumpyexpress.config.patch
dpkg-source: info: applying fix_shebang.patch
dpkg-source: info: applying do-not-override-dpkg-flags.patch
dpkg-source: info: applying cleanup-bin.patch

Check disk space
----------------

Sufficient free space for build

User Environment
----------------

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.i386
DEB_BUILD_OPTIONS=nocheck
HOME=/var/lib/sbuild
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmut
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SHELL=/bin/sh
USER=helmut

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -ai386 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package lumpy-sv
dpkg-buildpackage: info: source version 0.3.1+dfsg-8
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Nilesh Patra <nilesh@debian.org>
dpkg-architecture: warning: specified GNU system type i686-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture i386
 debian/rules clean
dh clean
   dh_auto_clean
	make -j1 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
Cleaning up.
make --no-print-directory -C src/filter/ clean
rm -vf lumpy_filter
#rm -Rf /lib
#rm -f /src/api/*.o
#rm -f /src/api/internal/*.o
#rm -Rf /include
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   dh_auto_build -a
	make -j1 INSTALL="install --strip-program=true" PKG_CONFIG=i686-linux-gnu-pkg-config CXX=i686-linux-gnu-g\+\+ CC=i686-linux-gnu-gcc
make[1]: Entering directory '/<<PKGBUILDDIR>>'
[ -d bin ] || mkdir -p bin
make --no-print-directory -C src/filter/
i686-linux-gnu-gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -I/usr/include/htslib -o lumpy_filter filter.c -lhts -lcrypto -lcurl -lpthread -lz -Wl,-z,relro -Wl,-z,now
cp src/filter/lumpy_filter bin
[ -d bin ] || mkdir -p bin
cp scripts/lumpyexpress bin/lumpyexpress
> bin/lumpyexpress.config
[ -d obj ] || mkdir -p obj
[ -d bin ] || mkdir -p bin
Building lumpy:
=========================================================
#make --no-print-directory --directory= api
for dir in src/utils/bedFile src/utils/version src/utils/fileType src/utils/bedFilePE src/utils/genomeFile src/utils/BamTools-Ancillary src/utils/sequenceUtilities ; do \
	echo "- Building in $dir"; \
	make --no-print-directory -C $dir; \
	echo ""; \
done
- Building in src/utils/bedFile
  * compiling bedFile.cpp
In file included from bedFile.cpp:12:
bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^

- Building in src/utils/version
  * compiling version.cpp

- Building in src/utils/fileType
  * compiling fileType.cpp

- Building in src/utils/bedFilePE
  * compiling bedFilePE.cpp
In file included from bedFilePE.h:12,
                 from bedFilePE.cpp:15:
../../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^

- Building in src/utils/genomeFile
  * compiling genomeFile.cpp
genomeFile.cpp: In member function ‘void GenomeFile::loadGenomeFileIntoMap()’:
genomeFile.cpp:61:26: warning: variable ‘c2’ set but not used [-Wunused-but-set-variable]
   61 |                     long c2;
      |                          ^~

- Building in src/utils/BamTools-Ancillary
  * compiling BamAncillary.cpp
In file included from BamAncillary.h:12,
                 from BamAncillary.cpp:12:
..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
  * compiling BamAncillary.cpp
In file included from BamAncillary.h:12,
                 from BamAncillary.cpp:12:
..//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
..//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^

- Building in src/utils/sequenceUtilities
  * compiling sequenceUtils.cpp

- Building in src/lumpy
  * compiling lumpy.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack lumpy.cpp -o ../../obj//lumpy.o
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
                 from lumpy.cpp:20:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
In file included from SV_BreakPoint.h:19,
                 from SV_Evidence.h:22,
                 from lumpy.cpp:24:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
In file included from SV_Evidence.h:24:
SV_EvidenceReader.h: At global scope:
SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins<SV_BreakPoint*>&)’ was hidden [-Woverloaded-virtual=]
   57 |     virtual void process_input( BamAlignment &_bam,
      |                  ^~~~~~~~~~~~~
In file included from SV_Bedpe.h:19,
                 from lumpy.cpp:27:
SV_BedpeReader.h:72:14: note:   by ‘void SV_BedpeReader::process_input(UCSCBins<SV_BreakPoint*>&)’
   72 |         void process_input( UCSCBins<SV_BreakPoint*> &r_bin);
      |              ^~~~~~~~~~~~~
SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins<SV_BreakPoint*>&)’ was hidden [-Woverloaded-virtual=]
   53 |     virtual void process_input( BamAlignment &_bam,
      |                  ^~~~~~~~~~~~~
SV_BedpeReader.h:72:14: note:   by ‘void SV_BedpeReader::process_input(UCSCBins<SV_BreakPoint*>&)’
   72 |         void process_input( UCSCBins<SV_BreakPoint*> &r_bin);
      |              ^~~~~~~~~~~~~
  * compiling SV_Pair.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Pair.cpp -o ../../obj//SV_Pair.o
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
                 from SV_Pair.cpp:15:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
In file included from SV_BreakPoint.h:19,
                 from SV_PairReader.h:22,
                 from SV_Pair.cpp:19:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
  * compiling SV_Evidence.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Evidence.cpp -o ../../obj//SV_Evidence.o
In file included from SV_BreakPoint.h:19,
                 from SV_Evidence.h:22,
                 from SV_Evidence.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
SV_Evidence.cpp: In member function ‘virtual void SV_Evidence::set_bp_interval_probability(breakpoint_interval*)’:
SV_Evidence.cpp:81:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
   81 |     for (j = 0; j < size; ++j) {
      |                 ~~^~~~~~
  * compiling SV_BreakPoint.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BreakPoint.cpp -o ../../obj//SV_BreakPoint.o
In file included from SV_BreakPoint.h:19,
                 from SV_BreakPoint.cpp:16:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
SV_BreakPoint.cpp: In member function ‘bool SV_BreakPoint::merge(SV_BreakPoint*)’:
SV_BreakPoint.cpp:266:33: warning: variable ‘a_overlap_intr’ set but not used [-Wunused-but-set-variable]
  266 |     struct breakpoint_interval *a_overlap_intr, *b_overlap_intr;
      |                                 ^~~~~~~~~~~~~~
SV_BreakPoint.cpp:266:50: warning: variable ‘b_overlap_intr’ set but not used [-Wunused-but-set-variable]
  266 |     struct breakpoint_interval *a_overlap_intr, *b_overlap_intr;
      |                                                  ^~~~~~~~~~~~~~
../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS) [with T = SV_BreakPoint*; BIN = unsigned int; CHR_POS = long long unsigned int]’:
../utils//UCSCBins/ucsc_bins.hpp:238:18:   required from ‘void UCSCBins<T>::add(std::string, CHR_POS, CHR_POS, char, T) [with T = SV_BreakPoint*; std::string = std::__cxx11::basic_string<char>; CHR_POS = long long unsigned int]’
  238 |         BIN bin = getBin(start, end);
      |                   ~~~~~~^~~~~~~~~~~~
SV_BreakPoint.cpp:1286:14:   required from here
 1286 |     r_bin.add(interval_r.i.chr,
      |     ~~~~~~~~~^~~~~~~~~~~~~~~~~~
 1287 |               interval_r.i.start,
      |               ~~~~~~~~~~~~~~~~~~~
 1288 |               interval_r.i.end,
      |               ~~~~~~~~~~~~~~~~~
 1289 |               interval_r.i.strand,
      |               ~~~~~~~~~~~~~~~~~~~~
 1290 |               this);
      |               ~~~~~
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
SV_BreakPoint.cpp: In static member function ‘static void SV_BreakPoint::trim_interval(log_space*, unsigned int, int*, int*)’:
SV_BreakPoint.cpp:704:24: warning: ‘max_i’ may be used uninitialized [-Wmaybe-uninitialized]
  704 |     if ((l == r) && (l == max_i))
      |                     ~~~^~~~~~~~~
SV_BreakPoint.cpp:667:21: note: ‘max_i’ was declared here
  667 |     unsigned int i, max_i;
      |                     ^~~~~
SV_BreakPoint.cpp: In static member function ‘static int SV_BreakPoint::get_product(std::vector<SV_BreakPoint*>&, CHR_POS*, CHR_POS*, CHR_POS*, CHR_POS*, log_space**, log_space**)’:
SV_BreakPoint.cpp:1650:41: warning: ‘l_max_i’ may be used uninitialized [-Wmaybe-uninitialized]
 1650 |         CHR_POS abs_max_l = m_start_l + l_max_i;
      |                                         ^~~~~~~
SV_BreakPoint.cpp:1643:25: note: ‘l_max_i’ was declared here
 1643 |         unsigned int i, l_max_i, r_max_i;
      |                         ^~~~~~~
SV_BreakPoint.cpp:1662:41: warning: ‘r_max_i’ may be used uninitialized [-Wmaybe-uninitialized]
 1662 |         CHR_POS abs_max_r = m_start_r + r_max_i;
      |                                         ^~~~~~~
SV_BreakPoint.cpp:1643:34: note: ‘r_max_i’ was declared here
 1643 |         unsigned int i, l_max_i, r_max_i;
      |                                  ^~~~~~~
  * compiling SV_Bedpe.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Bedpe.cpp -o ../../obj//SV_Bedpe.o
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
                 from SV_Bedpe.cpp:14:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
In file included from SV_BedpeReader.h:21,
                 from SV_Bedpe.cpp:17:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
In file included from SV_BedpeReader.h:22:
SV_EvidenceReader.h: At global scope:
SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins<SV_BreakPoint*>&)’ was hidden [-Woverloaded-virtual=]
   53 |     virtual void process_input( BamAlignment &_bam,
      |                  ^~~~~~~~~~~~~
SV_BedpeReader.h:72:14: note:   by ‘void SV_BedpeReader::process_input(UCSCBins<SV_BreakPoint*>&)’
   72 |         void process_input( UCSCBins<SV_BreakPoint*> &r_bin);
      |              ^~~~~~~~~~~~~
SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins<SV_BreakPoint*>&)’ was hidden [-Woverloaded-virtual=]
   57 |     virtual void process_input( BamAlignment &_bam,
      |                  ^~~~~~~~~~~~~
SV_BedpeReader.h:72:14: note:   by ‘void SV_BedpeReader::process_input(UCSCBins<SV_BreakPoint*>&)’
   72 |         void process_input( UCSCBins<SV_BreakPoint*> &r_bin);
      |              ^~~~~~~~~~~~~
  * compiling SV_SplitRead.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitRead.cpp -o ../../obj//SV_SplitRead.o
In file included from ../utils//BamTools-Ancillary/BamAncillary.h:12,
                 from SV_SplitRead.cpp:15:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
In file included from SV_BreakPoint.h:19,
                 from SV_SplitReadReader.h:22,
                 from SV_SplitRead.cpp:19:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
SV_SplitRead.cpp: In member function ‘bool SV_SplitRead::is_sane()’:
SV_SplitRead.cpp:538:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  538 |     if ( min_mapping_quality < reader->min_mapping_threshold )
      |          ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
SV_SplitRead.cpp: In static member function ‘static void SV_SplitRead::process_split(const BamTools::BamAlignment&, BamTools::RefVector, std::map<std::__cxx11::basic_string<char>, BamTools::BamAlignment>&, UCSCBins<SV_BreakPoint*>&, int, int, SV_SplitReadReader*)’:
SV_SplitRead.cpp:653:25: warning: ‘void free(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  653 |                     free(new_split_read);
      |                     ~~~~^~~~~~~~~~~~~~~~
SV_SplitRead.cpp:641:41: note: returned from ‘void* operator new(std::size_t)’
  641 |                                  _reader);
      |                                         ^
  * compiling SV_SplitReadReader.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_SplitReadReader.cpp -o ../../obj//SV_SplitReadReader.o
In file included from SV_BreakPoint.h:19,
                 from SV_SplitReadReader.h:22,
                 from SV_SplitReadReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
                 from SV_SplitRead.h:27,
                 from SV_SplitReadReader.cpp:16:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
  * compiling SV_PairReader.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_PairReader.cpp -o ../../obj//SV_PairReader.o
In file included from SV_BreakPoint.h:19,
                 from SV_PairReader.h:22,
                 from SV_PairReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
  * compiling SV_BedpeReader.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BedpeReader.cpp -o ../../obj//SV_BedpeReader.o
In file included from SV_BreakPoint.h:19,
                 from SV_Evidence.h:22,
                 from SV_Bedpe.h:18,
                 from SV_BedpeReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
                 from SV_BedpeReader.h:23,
                 from SV_Bedpe.h:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
In file included from SV_Evidence.h:24:
SV_EvidenceReader.h: At global scope:
SV_EvidenceReader.h:53:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, BamTools::BamWriter&, UCSCBins<SV_BreakPoint*>&)’ was hidden [-Woverloaded-virtual=]
   53 |     virtual void process_input( BamAlignment &_bam,
      |                  ^~~~~~~~~~~~~
SV_BedpeReader.h:72:14: note:   by ‘void SV_BedpeReader::process_input(UCSCBins<SV_BreakPoint*>&)’
   72 |         void process_input( UCSCBins<SV_BreakPoint*> &r_bin);
      |              ^~~~~~~~~~~~~
SV_EvidenceReader.h:57:18: warning: ‘virtual void SV_EvidenceReader::process_input(BamTools::BamAlignment&, BamTools::RefVector&, UCSCBins<SV_BreakPoint*>&)’ was hidden [-Woverloaded-virtual=]
   57 |     virtual void process_input( BamAlignment &_bam,
      |                  ^~~~~~~~~~~~~
SV_BedpeReader.h:72:14: note:   by ‘void SV_BedpeReader::process_input(UCSCBins<SV_BreakPoint*>&)’
   72 |         void process_input( UCSCBins<SV_BreakPoint*> &r_bin);
      |              ^~~~~~~~~~~~~
  * compiling SV_BamReader.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_BamReader.cpp -o ../../obj//SV_BamReader.o
In file included from SV_BreakPoint.h:19,
                 from SV_PairReader.h:22,
                 from SV_BamReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
                 from SV_SplitRead.h:27,
                 from SV_BamReader.cpp:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
SV_BamReader.cpp: In member function ‘virtual void SV_BamReader::process_input_chr_pos(std::string, CHR_POS, UCSCBins<SV_BreakPoint*>&)’:
SV_BamReader.cpp:208:28: warning: comparison of integer expressions of different signedness: ‘int32_t’ {aka ‘int’} and ‘CHR_POS’ {aka ‘long long unsigned int’} [-Wsign-compare]
  208 |             ( bam.Position < pos ) ) {
      |               ~~~~~~~~~~~~~^~~~~
  * compiling SV_InterChromBamReader.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_InterChromBamReader.cpp -o ../../obj//SV_InterChromBamReader.o
In file included from SV_BreakPoint.h:19,
                 from SV_PairReader.h:22,
                 from SV_InterChromBamReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
In file included from ../utils//bedFilePE/bedFilePE.h:12,
                 from SV_SplitRead.h:27,
                 from SV_InterChromBamReader.cpp:19:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
  * compiling SV_EvidenceReader.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_EvidenceReader.cpp -o ../../obj//SV_EvidenceReader.o
In file included from SV_EvidenceReader.h:20,
                 from SV_EvidenceReader.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
  * compiling SV_Tools.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_Tools.cpp -o ../../obj//SV_Tools.o
In file included from SV_Tools.h:19,
                 from SV_Tools.cpp:24:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
In file included from SV_Tools.cpp:27:
../utils//bedFile/bedFile.h: In function ‘BIN getBin(CHRPOS, CHRPOS)’:
../utils//bedFile/bedFile.h:321:25: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  321 |     for (register short i = 0; i < _binLevels; ++i) {
      |                         ^
../utils//UCSCBins/ucsc_bins.hpp: In instantiation of ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS) [with T = int; BIN = unsigned int; CHR_POS = long long unsigned int]’:
../utils//UCSCBins/ucsc_bins.hpp:238:18:   required from ‘void UCSCBins<T>::add(std::string, CHR_POS, CHR_POS, char, T) [with T = int; std::string = std::__cxx11::basic_string<char>; CHR_POS = long long unsigned int]’
  238 |         BIN bin = getBin(start, end);
      |                   ~~~~~~^~~~~~~~~~~~
SV_Tools.cpp:541:32:   required from here
  541 |             exclude_regions.add(bed.chrom,
      |             ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~
  542 |                                 bed.start,
      |                                 ~~~~~~~~~~
  543 |                                 bed.end,
      |                                 ~~~~~~~~
  544 |                                 '+',
      |                                 ~~~~
  545 |                                 1);
      |                                 ~~
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
SV_Tools.cpp: In function ‘int read_distro_file(std::string, double**, int*, int*)’:
SV_Tools.cpp:156:14: warning: ‘last’ may be used uninitialized [-Wmaybe-uninitialized]
  156 |         *end = last;
      |         ~~~~~^~~~~~
SV_Tools.cpp:143:13: note: ‘last’ was declared here
  143 |         int last;
      |             ^~~~
  * compiling SV_VcfVariant.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack SV_VcfVariant.cpp -o ../../obj//SV_VcfVariant.o
In file included from SV_BreakPoint.h:19,
                 from SV_VcfVariant.h:18,
                 from SV_VcfVariant.cpp:15:
../utils//UCSCBins/ucsc_bins.hpp: In static member function ‘static BIN UCSCBins<T>::getBin(CHR_POS, CHR_POS)’:
../utils//UCSCBins/ucsc_bins.hpp:253:29: warning: ISO C++17 does not allow ‘register’ storage class specifier [-Wregister]
  253 |         for (register short i = 0; i < kBinLevels; ++i) {
      |                             ^
  * compiling log_space.cpp
i686-linux-gnu-g++ -g  -c -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -I../utils//bedFile/ -I../utils//bedFilePE/ -I../utils//genomeFile/ -I../utils//version/ -I../utils//lineFileUtilities/ -I../utils//fileType/ -I/usr/include/bamtools -I../utils//BamTools-Ancillary -I../utils//sequenceUtilities -I../utils//UCSCBins -I/usr/include/fastahack log_space.cpp -o ../../obj//log_space.o
  * linking lumpy
i686-linux-gnu-g++ -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC -Wdate-time -D_FORTIFY_SOURCE=2 -o ../../bin//lumpy ../../obj//lumpy.o ../../obj//SV_Pair.o ../../obj//SV_Evidence.o ../../obj//SV_BreakPoint.o ../../obj//SV_Bedpe.o ../../obj//SV_SplitRead.o ../../obj//SV_SplitReadReader.o ../../obj//SV_PairReader.o ../../obj//SV_BedpeReader.o ../../obj//SV_BamReader.o ../../obj//SV_InterChromBamReader.o ../../obj//SV_EvidenceReader.o ../../obj//SV_Tools.o ../../obj//SV_VcfVariant.o ../../obj//log_space.o ../../obj//BamAncillary.o ../../obj//sequenceUtils.o ../../obj//bedFilePE.o ../../obj//bedFile.o ../../obj//genomeFile.o ../../obj//fileType.o \
	-L../utils//BamTools/lib/ -lbamtools \
	-lz -L /<<PKGBUILDDIR>>/debian/.debhelper/generated/_source/home/src/zlib-1.2.8 \
	-lgzstream -lz -lm -ldl -lpthread

make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh: command-omitted: The call to "dh_auto_test -a" was omitted due to "DEB_BUILD_OPTIONS=nocheck"
   create-stamp debian/debhelper-build-stamp
   dh_prep -a
   dh_auto_install -a
   debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cat debian/missing-sources/pe.pos_sorted.sam |samtools view -Sb - > data/pe.pos_sorted.bam
/bin/sh: 1: samtools: Exec format error
make[1]: *** [debian/rules:20: override_dh_install] Error 126
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:11: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2025-11-05T17:39:56Z

+------------------------------------------------------------------------------+
| Finished Timed Build Commands                                                |
+------------------------------------------------------------------------------+


rm -Rf /<<PKGBUILDDIR>>/
--------------------------------------------------


I: Finished running 'rm -Rf /<<PKGBUILDDIR>>/'.

Finished processing commands.
--------------------------------------------------------------------------------

Finished
--------


+------------------------------------------------------------------------------+
| Cleanup                                                                      |
+------------------------------------------------------------------------------+

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

+------------------------------------------------------------------------------+
| Summary                                                                      |
+------------------------------------------------------------------------------+

Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any
Build-Space: n/a
Build-Time: 226
Distribution: unstable
Fail-Stage: build
Foreign Architectures: i386
Host Architecture: i386
Install-Time: 52
Job: lumpy-sv_0.3.1+dfsg-8
Machine Architecture: arm64
Package: lumpy-sv
Package-Time: 320
Source-Version: 0.3.1+dfsg-8
Space: n/a
Status: attempted
Version: 0.3.1+dfsg-8
--------------------------------------------------------------------------------
Finished at 2025-11-05T17:39:56Z
Build needed 00:05:20, no disk space