Artifact sibelia_3.0.7+dfsg-3_arm64-2024-11-23T10:29:04Z

Metadata
bd_uninstallable: null
filename: sibelia_3.0.7+dfsg-3_arm64-2024-11-23T10:29:04Z.build
source: sibelia
version: 3.0.7+dfsg-3

File

sibelia_3.0.7+dfsg-3_arm64-2024-11-23T10:29:04Z.build
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sbuild (Debian sbuild) 0.86.3~bpo12+1 (03 November 2024) on debusine-worker-arm64-demeter-05.freexian.com

+==============================================================================+
| sibelia 3.0.7+dfsg-3 (arm64)                 Sat, 23 Nov 2024 10:29:04 +0000 |
+==============================================================================+

Package: sibelia
Version: 3.0.7+dfsg-3
Source Version: 3.0.7+dfsg-3
Distribution: sid
Machine Architecture: arm64
Host Architecture: arm64
Build Architecture: arm64
Build Type: binary

I: No tarballs found in /var/lib/debusine/worker/.cache/sbuild
Unpacking /var/lib/debusine/worker/system-images/1053884/system.tar.xz to /tmp/tmp.sbuild.y7cV9W8FC9...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'

+------------------------------------------------------------------------------+
| Chroot Setup Commands                                                        |
+------------------------------------------------------------------------------+


rm -f /etc/resolv.conf
----------------------


I: Finished running 'rm -f /etc/resolv.conf'.

Finished processing commands.
--------------------------------------------------------------------------------
Copying /tmp/debusine-fetch-exec-upload-qm6wlalt/seqan-apps-dbgsym_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-qm6wlalt/seqan-apps_2.5.0~rc3+dfsg-1_arm64.deb to /<<CHROOT>>...
Copying /tmp/debusine-fetch-exec-upload-qm6wlalt/libseqan2-dev_2.5.0~rc3+dfsg-1_all.deb to /<<CHROOT>>...
I: NOTICE: Log filtering will replace 'build/sibelia-OXdysG/resolver-hA2pqt' with '<<RESOLVERDIR>>'

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

Get:1 file:/build/sibelia-OXdysG/resolver-02lzlI/apt_archive ./ InRelease
Ign:1 file:/build/sibelia-OXdysG/resolver-02lzlI/apt_archive ./ InRelease
Get:2 file:/build/sibelia-OXdysG/resolver-02lzlI/apt_archive ./ Release [606 B]
Get:3 http://deb.debian.org/debian sid InRelease [202 kB]
Get:2 file:/build/sibelia-OXdysG/resolver-02lzlI/apt_archive ./ Release [606 B]
Get:4 file:/build/sibelia-OXdysG/resolver-02lzlI/apt_archive ./ Release.gpg
Ign:4 file:/build/sibelia-OXdysG/resolver-02lzlI/apt_archive ./ Release.gpg
Get:5 file:/build/sibelia-OXdysG/resolver-02lzlI/apt_archive ./ Packages [4687 B]
Get:6 http://deb.debian.org/debian sid/main arm64 Packages [9958 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 Components [4913 kB]
Fetched 15.1 MB in 2s (6439 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
  apt base-files libapt-pkg6.0t64 libxml-sax-perl
4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 2411 kB of archives.
After this operation, 206 kB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main arm64 base-files arm64 13.6 [72.9 kB]
Get:2 http://deb.debian.org/debian sid/main arm64 libapt-pkg6.0t64 arm64 2.9.14 [969 kB]
Get:3 http://deb.debian.org/debian sid/main arm64 apt arm64 2.9.14 [1316 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-4 [53.4 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2411 kB in 0s (30.4 MB/s)
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(Reading database ... 17119 files and directories currently installed.)
Preparing to unpack .../base-files_13.6_arm64.deb ...
Unpacking base-files (13.6) over (13.5) ...
Setting up base-files (13.6) ...
Updating /root/.profile to current default.
(Reading database ... 
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(Reading database ... 17119 files and directories currently installed.)
Preparing to unpack .../libapt-pkg6.0t64_2.9.14_arm64.deb ...
Unpacking libapt-pkg6.0t64:arm64 (2.9.14) over (2.9.12) ...
Setting up libapt-pkg6.0t64:arm64 (2.9.14) ...
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Preparing to unpack .../archives/apt_2.9.14_arm64.deb ...
Unpacking apt (2.9.14) over (2.9.12) ...
Setting up apt (2.9.14) ...
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(Reading database ... 17119 files and directories currently installed.)
Preparing to unpack .../libxml-sax-perl_1.02+dfsg-4_all.deb ...
Unpacking libxml-sax-perl (1.02+dfsg-4) over (1.02+dfsg-3) ...
Setting up libxml-sax-perl (1.02+dfsg-4) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for libc-bin (2.40-3) ...

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


Local sources
-------------

/tmp/debusine-fetch-exec-upload-qm6wlalt/sibelia_3.0.7+dfsg-3.dsc exists in /tmp/debusine-fetch-exec-upload-qm6wlalt; copying to chroot
I: NOTICE: Log filtering will replace 'build/sibelia-OXdysG/sibelia-3.0.7+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/sibelia-OXdysG' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev, libseqan2-dev, libtclap-dev, libhts-dev, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev, libseqan2-dev, libtclap-dev, libhts-dev, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [698 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [730 B]
Fetched 2037 B in 0s (185 kB/s)
Reading package lists...
Ign:1 file:/<<BUILDDIR>>/resolver-02lzlI/apt_archive ./ InRelease
Get:2 file:/<<BUILDDIR>>/resolver-02lzlI/apt_archive ./ Release [606 B]
Get:2 file:/<<BUILDDIR>>/resolver-02lzlI/apt_archive ./ Release [606 B]
Ign:3 file:/<<BUILDDIR>>/resolver-02lzlI/apt_archive ./ Release.gpg
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev build-essential cmake cmake-data
  comerr-dev cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
  debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot g++ g++-14
  g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
  gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu krb5-multidev libarchive13t64
  libasan8 libboost-dev libboost1.83-dev libbrotli-dev libbz2-dev libc-dev-bin
  libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev libcurl4t64
  libdebhelper-perl libdeflate-dev libdeflate0 libdivsufsort-dev
  libdivsufsort3 libelf1t64 libevent-2.1-7t64 libexpat1 libfakeroot
  libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl
  libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssrpc4t64
  libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1
  libjsoncpp26 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkrb5-dev
  libldap-dev liblsan0 liblzma-dev libmpc3 libmpfr6 libncursesw6
  libnghttp2-dev libnghttp3-dev libngtcp2-crypto-gnutls-dev libngtcp2-dev
  libp11-kit-dev libpkgconf3 libproc2-0 libpsl-dev librhash1 librtmp-dev
  libseqan2-dev libssh2-1-dev libssl-dev libstdc++-14-dev libtasn1-6-dev
  libtclap-dev libtool libtsan2 libubsan1 libunbound8 libuv1t64 libzstd-dev
  linux-libc-dev m4 nettle-dev pkgconf pkgconf-bin po-debconf procps
  rpcsvc-proto zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc cmake-doc cmake-format
  elpa-cmake-mode ninja-build doc-base cpp-doc gcc-14-locales cpp-14-doc
  dh-make gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
  gdb-aarch64-linux-gnu krb5-doc lrzip libboost-doc libboost1.83-doc
  libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev
  libboost-context1.83-dev libboost-contract1.83-dev
  libboost-coroutine1.83-dev libboost-date-time1.83-dev
  libboost-exception1.83-dev libboost-fiber1.83-dev
  libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev
  libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev
  libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev
  libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev
  libboost-numpy1.83-dev libboost-program-options1.83-dev
  libboost-python1.83-dev libboost-random1.83-dev libboost-regex1.83-dev
  libboost-serialization1.83-dev libboost-stacktrace1.83-dev
  libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev
  libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev
  libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev
  libc-devtools glibc-doc libcurl4-doc libidn-dev gmp-doc libgmp10-doc
  libmpfr-dev dns-root-data gnutls-bin gnutls-doc krb5-user liblzma-doc
  libnghttp2-doc p11-kit-doc libssl-doc libstdc++-14-doc libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc libmail-box-perl
Recommended packages:
  bzip2-doc manpages manpages-dev libarchive-cpio-perl libgpm2 libtasn1-doc
  libltdl-dev libmail-sendmail-perl psmisc linux-sysctl-defaults
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev build-essential cmake cmake-data
  comerr-dev cpp cpp-14 cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu
  debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot g++ g++-14
  g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc gcc-14
  gcc-14-aarch64-linux-gnu gcc-aarch64-linux-gnu krb5-multidev libarchive13t64
  libasan8 libboost-dev libboost1.83-dev libbrotli-dev libbz2-dev libc-dev-bin
  libc6-dev libcc1-0 libcrypt-dev libcurl4-gnutls-dev libcurl4t64
  libdebhelper-perl libdeflate-dev libdeflate0 libdivsufsort-dev
  libdivsufsort3 libelf1t64 libevent-2.1-7t64 libexpat1 libfakeroot
  libfile-stripnondeterminism-perl libgcc-14-dev libgmp-dev libgmpxx4ldbl
  libgnutls-dane0t64 libgnutls-openssl27t64 libgnutls28-dev libgssrpc4t64
  libhts-dev libhts3t64 libhtscodecs2 libhwasan0 libidn2-dev libisl23 libitm1
  libjsoncpp26 libkadm5clnt-mit12 libkadm5srv-mit12 libkdb5-10t64 libkrb5-dev
  libldap-dev liblsan0 liblzma-dev libmpc3 libmpfr6 libncursesw6
  libnghttp2-dev libnghttp3-dev libngtcp2-crypto-gnutls-dev libngtcp2-dev
  libp11-kit-dev libpkgconf3 libproc2-0 libpsl-dev librhash1 librtmp-dev
  libseqan2-dev libssh2-1-dev libssl-dev libstdc++-14-dev libtasn1-6-dev
  libtclap-dev libtool libtsan2 libubsan1 libunbound8 libuv1t64 libzstd-dev
  linux-libc-dev m4 nettle-dev pkgconf pkgconf-bin po-debconf procps
  rpcsvc-proto sbuild-build-depends-main-dummy zlib1g-dev
0 upgraded, 105 newly installed, 0 to remove and 0 not upgraded.
Need to get 104 MB/106 MB of archives.
After this operation, 537 MB of additional disk space will be used.
Get:1 file:/<<BUILDDIR>>/resolver-02lzlI/apt_archive ./ libseqan2-dev 2.5.0~rc3+dfsg-1 [1222 kB]
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [924 B]
Get:3 http://deb.debian.org/debian sid/main arm64 libncursesw6 arm64 6.5-2+b1 [125 kB]
Get:4 http://deb.debian.org/debian sid/main arm64 libproc2-0 arm64 2:4.0.4-6 [62.3 kB]
Get:5 http://deb.debian.org/debian sid/main arm64 procps arm64 2:4.0.4-6 [872 kB]
Get:6 http://deb.debian.org/debian sid/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:7 http://deb.debian.org/debian sid/main arm64 autoconf all 2.72-3 [493 kB]
Get:8 http://deb.debian.org/debian sid/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:9 http://deb.debian.org/debian sid/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:10 http://deb.debian.org/debian sid/main arm64 autopoint all 0.22.5-2 [723 kB]
Get:11 http://deb.debian.org/debian sid/main arm64 libc-dev-bin arm64 2.40-3 [50.9 kB]
Get:12 http://deb.debian.org/debian sid/main arm64 linux-libc-dev all 6.11.9-1 [2459 kB]
Get:13 http://deb.debian.org/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB]
Get:14 http://deb.debian.org/debian sid/main arm64 rpcsvc-proto arm64 1.4.3-1+b1 [60.5 kB]
Get:15 http://deb.debian.org/debian sid/main arm64 libc6-dev arm64 2.40-3 [1591 kB]
Get:16 http://deb.debian.org/debian sid/main arm64 libisl23 arm64 0.27-1 [601 kB]
Get:17 http://deb.debian.org/debian sid/main arm64 libmpfr6 arm64 4.2.1-1+b2 [680 kB]
Get:18 http://deb.debian.org/debian sid/main arm64 libmpc3 arm64 1.3.1-1+b3 [50.5 kB]
Get:19 http://deb.debian.org/debian sid/main arm64 cpp-14-aarch64-linux-gnu arm64 14.2.0-8 [9166 kB]
Get:20 http://deb.debian.org/debian sid/main arm64 cpp-14 arm64 14.2.0-8 [1284 B]
Get:21 http://deb.debian.org/debian sid/main arm64 cpp-aarch64-linux-gnu arm64 4:14.2.0-1 [4832 B]
Get:22 http://deb.debian.org/debian sid/main arm64 cpp arm64 4:14.2.0-1 [1568 B]
Get:23 http://deb.debian.org/debian sid/main arm64 libcc1-0 arm64 14.2.0-8 [42.2 kB]
Get:24 http://deb.debian.org/debian sid/main arm64 libitm1 arm64 14.2.0-8 [24.2 kB]
Get:25 http://deb.debian.org/debian sid/main arm64 libasan8 arm64 14.2.0-8 [2579 kB]
Get:26 http://deb.debian.org/debian sid/main arm64 liblsan0 arm64 14.2.0-8 [1161 kB]
Get:27 http://deb.debian.org/debian sid/main arm64 libtsan2 arm64 14.2.0-8 [2386 kB]
Get:28 http://deb.debian.org/debian sid/main arm64 libubsan1 arm64 14.2.0-8 [1039 kB]
Get:29 http://deb.debian.org/debian sid/main arm64 libhwasan0 arm64 14.2.0-8 [1442 kB]
Get:30 http://deb.debian.org/debian sid/main arm64 libgcc-14-dev arm64 14.2.0-8 [2365 kB]
Get:31 http://deb.debian.org/debian sid/main arm64 gcc-14-aarch64-linux-gnu arm64 14.2.0-8 [17.7 MB]
Get:32 http://deb.debian.org/debian sid/main arm64 gcc-14 arm64 14.2.0-8 [519 kB]
Get:33 http://deb.debian.org/debian sid/main arm64 gcc-aarch64-linux-gnu arm64 4:14.2.0-1 [1440 B]
Get:34 http://deb.debian.org/debian sid/main arm64 gcc arm64 4:14.2.0-1 [5136 B]
Get:35 http://deb.debian.org/debian sid/main arm64 libstdc++-14-dev arm64 14.2.0-8 [2267 kB]
Get:36 http://deb.debian.org/debian sid/main arm64 g++-14-aarch64-linux-gnu arm64 14.2.0-8 [10.1 MB]
Get:37 http://deb.debian.org/debian sid/main arm64 g++-14 arm64 14.2.0-8 [20.2 kB]
Get:38 http://deb.debian.org/debian sid/main arm64 g++-aarch64-linux-gnu arm64 4:14.2.0-1 [1200 B]
Get:39 http://deb.debian.org/debian sid/main arm64 g++ arm64 4:14.2.0-1 [1332 B]
Get:40 http://deb.debian.org/debian sid/main arm64 build-essential arm64 12.12 [4624 B]
Get:41 http://deb.debian.org/debian sid/main arm64 cmake-data all 3.31.1-1 [2267 kB]
Get:42 http://deb.debian.org/debian sid/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB]
Get:43 http://deb.debian.org/debian sid/main arm64 libcurl4t64 arm64 8.11.0-1 [322 kB]
Get:44 http://deb.debian.org/debian sid/main arm64 libexpat1 arm64 2.6.4-1 [90.7 kB]
Get:45 http://deb.debian.org/debian sid/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB]
Get:46 http://deb.debian.org/debian sid/main arm64 librhash1 arm64 1.4.5-1 [129 kB]
Get:47 http://deb.debian.org/debian sid/main arm64 libuv1t64 arm64 1.48.0-7 [143 kB]
Get:48 http://deb.debian.org/debian sid/main arm64 cmake arm64 3.31.1-1 [9873 kB]
Get:49 http://deb.debian.org/debian sid/main arm64 comerr-dev arm64 2.1-1.47.1-1+b1 [55.1 kB]
Get:50 http://deb.debian.org/debian sid/main arm64 libdebhelper-perl all 13.20 [89.7 kB]
Get:51 http://deb.debian.org/debian sid/main arm64 libtool all 2.4.7-8 [517 kB]
Get:52 http://deb.debian.org/debian sid/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:53 http://deb.debian.org/debian sid/main arm64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:54 http://deb.debian.org/debian sid/main arm64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:55 http://deb.debian.org/debian sid/main arm64 libelf1t64 arm64 0.192-4 [189 kB]
Get:56 http://deb.debian.org/debian sid/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:57 http://deb.debian.org/debian sid/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:58 http://deb.debian.org/debian sid/main arm64 debhelper all 13.20 [915 kB]
Get:59 http://deb.debian.org/debian sid/main arm64 libfakeroot arm64 1.36-1 [29.1 kB]
Get:60 http://deb.debian.org/debian sid/main arm64 fakeroot arm64 1.36-1 [74.4 kB]
Get:61 http://deb.debian.org/debian sid/main arm64 libgssrpc4t64 arm64 1.21.3-3 [56.7 kB]
Get:62 http://deb.debian.org/debian sid/main arm64 libkadm5clnt-mit12 arm64 1.21.3-3 [40.3 kB]
Get:63 http://deb.debian.org/debian sid/main arm64 libkdb5-10t64 arm64 1.21.3-3 [40.8 kB]
Get:64 http://deb.debian.org/debian sid/main arm64 libkadm5srv-mit12 arm64 1.21.3-3 [52.2 kB]
Get:65 http://deb.debian.org/debian sid/main arm64 krb5-multidev arm64 1.21.3-3 [126 kB]
Get:66 http://deb.debian.org/debian sid/main arm64 libboost1.83-dev arm64 1.83.0-3.2+b1 [10.6 MB]
Get:67 http://deb.debian.org/debian sid/main arm64 libboost-dev arm64 1.83.0.2+b2 [3828 B]
Get:68 http://deb.debian.org/debian sid/main arm64 libbrotli-dev arm64 1.1.0-2+b6 [308 kB]
Get:69 http://deb.debian.org/debian sid/main arm64 libbz2-dev arm64 1.0.8-6 [31.9 kB]
Get:70 http://deb.debian.org/debian sid/main arm64 libevent-2.1-7t64 arm64 2.1.12-stable-10+b1 [170 kB]
Get:71 http://deb.debian.org/debian sid/main arm64 libunbound8 arm64 1.22.0-1 [553 kB]
Get:72 http://deb.debian.org/debian sid/main arm64 libgnutls-dane0t64 arm64 3.8.8-2 [446 kB]
Get:73 http://deb.debian.org/debian sid/main arm64 libgnutls-openssl27t64 arm64 3.8.8-2 [446 kB]
Get:74 http://deb.debian.org/debian sid/main arm64 libidn2-dev arm64 2.3.7-2+b1 [122 kB]
Get:75 http://deb.debian.org/debian sid/main arm64 libp11-kit-dev arm64 0.25.5-2+b1 [208 kB]
Get:76 http://deb.debian.org/debian sid/main arm64 libtasn1-6-dev arm64 4.19.0-3+b3 [96.5 kB]
Get:77 http://deb.debian.org/debian sid/main arm64 libgmpxx4ldbl arm64 2:6.3.0+dfsg-2+b2 [329 kB]
Get:78 http://deb.debian.org/debian sid/main arm64 libgmp-dev arm64 2:6.3.0+dfsg-2+b2 [621 kB]
Get:79 http://deb.debian.org/debian sid/main arm64 nettle-dev arm64 3.10-1+b1 [1324 kB]
Get:80 http://deb.debian.org/debian sid/main arm64 libgnutls28-dev arm64 3.8.8-2 [1404 kB]
Get:81 http://deb.debian.org/debian sid/main arm64 libkrb5-dev arm64 1.21.3-3 [15.8 kB]
Get:82 http://deb.debian.org/debian sid/main arm64 libldap-dev arm64 2.5.18+dfsg-3+b1 [300 kB]
Get:83 http://deb.debian.org/debian sid/main arm64 libpkgconf3 arm64 1.8.1-4 [35.3 kB]
Get:84 http://deb.debian.org/debian sid/main arm64 pkgconf-bin arm64 1.8.1-4 [29.6 kB]
Get:85 http://deb.debian.org/debian sid/main arm64 pkgconf arm64 1.8.1-4 [26.1 kB]
Get:86 http://deb.debian.org/debian sid/main arm64 libnghttp2-dev arm64 1.64.0-1 [112 kB]
Get:87 http://deb.debian.org/debian sid/main arm64 libnghttp3-dev arm64 1.4.0-1+b1 [85.2 kB]
Get:88 http://deb.debian.org/debian sid/main arm64 libngtcp2-crypto-gnutls-dev arm64 1.6.0-1 [23.7 kB]
Get:89 http://deb.debian.org/debian sid/main arm64 libngtcp2-dev arm64 1.6.0-1 [165 kB]
Get:90 http://deb.debian.org/debian sid/main arm64 libpsl-dev arm64 0.21.2-1.1+b1 [77.9 kB]
Get:91 http://deb.debian.org/debian sid/main arm64 zlib1g-dev arm64 1:1.3.dfsg+really1.3.1-1+b1 [917 kB]
Get:92 http://deb.debian.org/debian sid/main arm64 librtmp-dev arm64 2.4+20151223.gitfa8646d.1-2+b5 [67.5 kB]
Get:93 http://deb.debian.org/debian sid/main arm64 libssl-dev arm64 3.3.2-2 [3185 kB]
Get:94 http://deb.debian.org/debian sid/main arm64 libssh2-1-dev arm64 1.11.1-1 [388 kB]
Get:95 http://deb.debian.org/debian sid/main arm64 libzstd-dev arm64 1.5.6+dfsg-1+b1 [329 kB]
Get:96 http://deb.debian.org/debian sid/main arm64 libcurl4-gnutls-dev arm64 8.11.0-1 [459 kB]
Get:97 http://deb.debian.org/debian sid/main arm64 libdeflate0 arm64 1.22-1 [42.2 kB]
Get:98 http://deb.debian.org/debian sid/main arm64 libdeflate-dev arm64 1.22-1 [51.2 kB]
Get:99 http://deb.debian.org/debian sid/main arm64 libdivsufsort3 arm64 2.0.1-6+b1 [39.9 kB]
Get:100 http://deb.debian.org/debian sid/main arm64 libdivsufsort-dev arm64 2.0.1-6+b1 [19.1 kB]
Get:101 http://deb.debian.org/debian sid/main arm64 libhtscodecs2 arm64 1.6.1-1 [74.6 kB]
Get:102 http://deb.debian.org/debian sid/main arm64 libhts3t64 arm64 1.20+ds-2 [420 kB]
Get:103 http://deb.debian.org/debian sid/main arm64 liblzma-dev arm64 5.6.3-1+b1 [312 kB]
Get:104 http://deb.debian.org/debian sid/main arm64 libhts-dev arm64 1.20+ds-2 [1626 kB]
Get:105 http://deb.debian.org/debian sid/main arm64 libtclap-dev arm64 1.2.5-1+b1 [3359 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 104 MB in 1s (83.2 MB/s)
Selecting previously unselected package libncursesw6:arm64.
(Reading database ... 17119 files and directories currently installed.)
Preparing to unpack .../000-libncursesw6_6.5-2+b1_arm64.deb ...
Unpacking libncursesw6:arm64 (6.5-2+b1) ...
Selecting previously unselected package libproc2-0:arm64.
Preparing to unpack .../001-libproc2-0_2%3a4.0.4-6_arm64.deb ...
Unpacking libproc2-0:arm64 (2:4.0.4-6) ...
Selecting previously unselected package procps.
Preparing to unpack .../002-procps_2%3a4.0.4-6_arm64.deb ...
Unpacking procps (2:4.0.4-6) ...
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Preparing to unpack .../003-m4_1.4.19-4_arm64.deb ...
Unpacking m4 (1.4.19-4) ...
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Preparing to unpack .../005-autotools-dev_20220109.1_all.deb ...
Unpacking autotools-dev (20220109.1) ...
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Preparing to unpack .../006-automake_1%3a1.16.5-1.3_all.deb ...
Unpacking automake (1:1.16.5-1.3) ...
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Setting up librhash1:arm64 (1.4.5-1) ...
Setting up libtsan2:arm64 (14.2.0-8) ...
Setting up libisl23:arm64 (0.27-1) ...
Setting up libc-dev-bin (2.40-3) ...
Setting up libdivsufsort3:arm64 (2.0.1-6+b1) ...
Setting up libtasn1-6-dev:arm64 (4.19.0-3+b3) ...
Setting up libdeflate-dev:arm64 (1.22-1) ...
Setting up libarchive13t64:arm64 (3.7.4-1.1) ...
Setting up libcc1-0:arm64 (14.2.0-8) ...
Setting up libbrotli-dev:arm64 (1.1.0-2+b6) ...
Setting up liblsan0:arm64 (14.2.0-8) ...
Setting up libp11-kit-dev:arm64 (0.25.5-2+b1) ...
Setting up libitm1:arm64 (14.2.0-8) ...
Setting up libdivsufsort-dev:arm64 (2.0.1-6+b1) ...
Setting up libkadm5clnt-mit12:arm64 (1.21.3-3) ...
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 libgmp-dev:arm64 (2:6.3.0+dfsg-2+b2) ...
Setting up nettle-dev:arm64 (3.10-1+b1) ...
Setting up libkdb5-10t64:arm64 (1.21.3-3) ...
Setting up pkgconf:arm64 (1.8.1-4) ...
Setting up cpp-14-aarch64-linux-gnu (14.2.0-8) ...
Setting up libkadm5srv-mit12:arm64 (1.21.3-3) ...
Setting up cmake (3.31.1-1) ...
Setting up libc6-dev:arm64 (2.40-3) ...
Setting up libgcc-14-dev:arm64 (14.2.0-8) ...
Setting up libstdc++-14-dev:arm64 (14.2.0-8) ...
Setting up libbz2-dev:arm64 (1.0.8-6) ...
Setting up libgnutls28-dev:arm64 (3.8.8-2) ...
Setting up libnghttp2-dev:arm64 (1.64.0-1) ...
Setting up libboost1.83-dev:arm64 (1.83.0-3.2+b1) ...
Setting up cpp-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up comerr-dev:arm64 (2.1-1.47.1-1+b1) ...
Setting up cpp-14 (14.2.0-8) ...
Setting up zlib1g-dev:arm64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up cpp (4:14.2.0-1) ...
Setting up libboost-dev:arm64 (1.83.0.2+b2) ...
Setting up gcc-14-aarch64-linux-gnu (14.2.0-8) ...
Setting up krb5-multidev:arm64 (1.21.3-3) ...
Setting up gcc-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up g++-14-aarch64-linux-gnu (14.2.0-8) ...
Setting up gcc-14 (14.2.0-8) ...
Setting up libkrb5-dev:arm64 (1.21.3-3) ...
Setting up librtmp-dev:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ...
Setting up libssh2-1-dev:arm64 (1.11.1-1) ...
Setting up g++-aarch64-linux-gnu (4:14.2.0-1) ...
Setting up g++-14 (14.2.0-8) ...
Setting up libtool (2.4.7-8) ...
Setting up libcurl4-gnutls-dev:arm64 (8.11.0-1) ...
Setting up gcc (4:14.2.0-1) ...
Setting up dh-autoreconf (20) ...
Setting up g++ (4:14.2.0-1) ...
update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode
Setting up build-essential (12.12) ...
Setting up libhts-dev:arm64 (1.20+ds-2) ...
Setting up debhelper (13.20) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for man-db (2.13.0-1) ...
Processing triggers for libc-bin (2.40-3) ...

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

Arch check ok (arm64 included in any all)

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

Kernel: Linux 6.1.0-27-cloud-arm64 #1 SMP Debian 6.1.115-1 (2024-11-01) arm64 (aarch64)
Toolchain package versions: binutils_2.43.1-5 dpkg-dev_1.22.11 g++-14_14.2.0-8 gcc-14_14.2.0-8 libc6-dev_2.40-3 libstdc++-14-dev_14.2.0-8 libstdc++6_14.2.0-8 linux-libc-dev_6.11.9-1
Package versions: appstream_1.0.3-1+b1 apt_2.9.14 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-2 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.5 bash_5.2.32-1+b2 binutils_2.43.1-5 binutils-aarch64-linux-gnu_2.43.1-5 binutils-common_2.43.1-5 bsdextrautils_2.40.2-11 bsdutils_1:2.40.2-11 build-essential_12.12 bzip2_1.0.8-6 ca-certificates_20240203 cmake_3.31.1-1 cmake-data_3.31.1-1 comerr-dev_2.1-1.47.1-1+b1 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-8 cpp-14-aarch64-linux-gnu_14.2.0-8 cpp-aarch64-linux-gnu_4:14.2.0-1 dash_0.5.12-9+b1 debconf_1.5.87 debhelper_13.20 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffstat_1.67-1 diffutils_1:3.10-1+b1 dpkg_1.22.11 dpkg-dev_1.22.11 dwz_0.15-1+b1 e2fsprogs_1.47.1-1+b1 fakeroot_1.36-1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-8 g++-14-aarch64-linux-gnu_14.2.0-8 g++-aarch64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-8 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+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


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

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Hash: SHA256

Format: 3.0 (quilt)
Source: sibelia
Binary: sibelia, sibelia-examples
Architecture: any all
Version: 3.0.7+dfsg-3
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: http://bioinf.spbau.ru/sibelia
Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/sibelia
Vcs-Git: https://salsa.debian.org/med-team/sibelia.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 12), cmake, libdivsufsort-dev, libboost-dev, libseqan2-dev, libtclap-dev, libhts-dev
Package-List:
 sibelia deb science optional arch=any
 sibelia-examples deb science optional arch=all
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-----END PGP SIGNATURE-----

gpgv: Signature made Tue Apr 14 08:37:29 2020 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tillea@rki.de"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./sibelia_3.0.7+dfsg-3.dsc: no acceptable signature found
dpkg-source: info: extracting sibelia in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking sibelia_3.0.7+dfsg.orig.tar.xz
dpkg-source: info: unpacking sibelia_3.0.7+dfsg-3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying use_debian_packaged_libdivsufsort.patch
dpkg-source: info: applying use_debian_packaged_lagan.patch
dpkg-source: info: applying snpeff_is_removed.patch
dpkg-source: info: applying 2to3.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=C.UTF-8
LC_ALL=C.UTF-8
LOGNAME=debusine-worker
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SHELL=/bin/sh
USER=debusine-worker

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

Command: dpkg-buildpackage --sanitize-env -us -uc -b -rfakeroot
dpkg-buildpackage: info: source package sibelia
dpkg-buildpackage: info: source version 3.0.7+dfsg-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 debian/rules clean
dh clean --sourcedirectory=src
   dh_auto_clean -O--sourcedirectory=src
   dh_autoreconf_clean -O--sourcedirectory=src
   dh_clean -O--sourcedirectory=src
 debian/rules binary
dh binary --sourcedirectory=src
   dh_update_autotools_config -O--sourcedirectory=src
   dh_autoreconf -O--sourcedirectory=src
   dh_auto_configure -O--sourcedirectory=src
	cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu ../src
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.10 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
  to tell CMake that the project requires at least <min> but has been updated
  to work with policies introduced by <max> or earlier.


-- The CXX compiler identification is GNU 14.2.0
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Configuring done (0.6s)
-- Generating done (0.0s)
CMake Warning:
  Manually-specified variables were not used by the project:

    CMAKE_EXPORT_NO_PACKAGE_REGISTRY
    CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
    CMAKE_FIND_USE_PACKAGE_REGISTRY
    CMAKE_INSTALL_LIBDIR
    CMAKE_INSTALL_LOCALSTATEDIR
    CMAKE_INSTALL_RUNSTATEDIR
    CMAKE_INSTALL_SYSCONFDIR
    FETCHCONTENT_FULLY_DISCONNECTED


-- Build files have been written to: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu
   dh_auto_build -O--sourcedirectory=src
	cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1
make[1]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
/usr/bin/cmake -S/<<PKGBUILDDIR>>/src -B/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/CMakeFiles /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu//CMakeFiles/progress.marks
make  -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make  -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
cd /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/src /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/CMakeFiles/Sibelia.dir/DependInfo.cmake "--color="
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make  -f CMakeFiles/Sibelia.dir/build.make CMakeFiles/Sibelia.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
[ 15%] Building CXX object CMakeFiles/Sibelia.dir/indexedsequence.cpp.o
[ 15%] Building CXX object CMakeFiles/Sibelia.dir/sibelia.cpp.o
[ 15%] Building CXX object CMakeFiles/Sibelia.dir/postprocessor.cpp.o
[ 20%] Building CXX object CMakeFiles/Sibelia.dir/util.cpp.o
[ 25%] Building CXX object CMakeFiles/Sibelia.dir/outputgenerator.cpp.o
[ 30%] Building CXX object CMakeFiles/Sibelia.dir/blockfinder.cpp.o
[ 35%] Building CXX object CMakeFiles/Sibelia.dir/blockinstance.cpp.o
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/sibelia.cpp.o -MF CMakeFiles/Sibelia.dir/sibelia.cpp.o.d -o CMakeFiles/Sibelia.dir/sibelia.cpp.o -c /<<PKGBUILDDIR>>/src/sibelia.cpp
[ 40%] Building CXX object CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/postprocessor.cpp.o -MF CMakeFiles/Sibelia.dir/postprocessor.cpp.o.d -o CMakeFiles/Sibelia.dir/postprocessor.cpp.o -c /<<PKGBUILDDIR>>/src/postprocessor.cpp
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -MF CMakeFiles/Sibelia.dir/indexedsequence.cpp.o.d -o CMakeFiles/Sibelia.dir/indexedsequence.cpp.o -c /<<PKGBUILDDIR>>/src/indexedsequence.cpp
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/util.cpp.o -MF CMakeFiles/Sibelia.dir/util.cpp.o.d -o CMakeFiles/Sibelia.dir/util.cpp.o -c /<<PKGBUILDDIR>>/src/util.cpp
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -MF CMakeFiles/Sibelia.dir/outputgenerator.cpp.o.d -o CMakeFiles/Sibelia.dir/outputgenerator.cpp.o -c /<<PKGBUILDDIR>>/src/outputgenerator.cpp
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockfinder.cpp.o -MF CMakeFiles/Sibelia.dir/blockfinder.cpp.o.d -o CMakeFiles/Sibelia.dir/blockfinder.cpp.o -c /<<PKGBUILDDIR>>/src/blockfinder.cpp
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/blockinstance.cpp.o -MF CMakeFiles/Sibelia.dir/blockinstance.cpp.o.d -o CMakeFiles/Sibelia.dir/blockinstance.cpp.o -c /<<PKGBUILDDIR>>/src/blockinstance.cpp
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -MF CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o.d -o CMakeFiles/Sibelia.dir/bifurcationstorage.cpp.o -c /<<PKGBUILDDIR>>/src/bifurcationstorage.cpp
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/fasta.h:10,
                 from /<<PKGBUILDDIR>>/src/dnasequence.h:10,
                 from /<<PKGBUILDDIR>>/src/bifurcationstorage.h:11,
                 from /<<PKGBUILDDIR>>/src/bifurcationstorage.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/fasta.h:10,
                 from /<<PKGBUILDDIR>>/src/dnasequence.h:10,
                 from /<<PKGBUILDDIR>>/src/hashing.h:10,
                 from /<<PKGBUILDDIR>>/src/indexedsequence.h:10,
                 from /<<PKGBUILDDIR>>/src/indexedsequence.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:10,
                 from /<<PKGBUILDDIR>>/src/blockfinder.h:10,
                 from /<<PKGBUILDDIR>>/src/util.h:10,
                 from /<<PKGBUILDDIR>>/src/util.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:10,
                 from /<<PKGBUILDDIR>>/src/blockinstance.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:10,
                 from /<<PKGBUILDDIR>>/src/blockfinder.h:10,
                 from /<<PKGBUILDDIR>>/src/blockfinder.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:10,
                 from /<<PKGBUILDDIR>>/src/blockfinder.h:10,
                 from /<<PKGBUILDDIR>>/src/util.h:10,
                 from /<<PKGBUILDDIR>>/src/outputgenerator.h:10,
                 from /<<PKGBUILDDIR>>/src/outputgenerator.cpp:9:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   37 |                 std::auto_ptr<DNASequence> sequence_;
      |                      ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
                 from /<<PKGBUILDDIR>>/src/common.h:20:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   38 |                 std::auto_ptr<BifurcationStorage> bifStorage_;
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/blockfinder.h:11:
/<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   37 |                 std::auto_ptr<DNASequence> sequence_;
      |                      ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
                 from /<<PKGBUILDDIR>>/src/common.h:20:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   38 |                 std::auto_ptr<BifurcationStorage> bifStorage_;
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/blockfinder.h:11:
/<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   37 |                 std::auto_ptr<DNASequence> sequence_;
      |                      ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
                 from /<<PKGBUILDDIR>>/src/common.h:20:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   38 |                 std::auto_ptr<BifurcationStorage> bifStorage_;
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/blockfinder.h:11:
/<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   37 |                 std::auto_ptr<DNASequence> sequence_;
      |                      ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
                 from /<<PKGBUILDDIR>>/src/common.h:20:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   38 |                 std::auto_ptr<BifurcationStorage> bifStorage_;
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
[ 45%] Building CXX object CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -MF CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o.d -o CMakeFiles/Sibelia.dir/bulgeremoval.cpp.o -c /<<PKGBUILDDIR>>/src/bulgeremoval.cpp
[ 50%] Building CXX object CMakeFiles/Sibelia.dir/dnasequence.cpp.o
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/dnasequence.cpp.o -MF CMakeFiles/Sibelia.dir/dnasequence.cpp.o.d -o CMakeFiles/Sibelia.dir/dnasequence.cpp.o -c /<<PKGBUILDDIR>>/src/dnasequence.cpp
[ 55%] Building CXX object CMakeFiles/Sibelia.dir/edge.cpp.o
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/edge.cpp.o -MF CMakeFiles/Sibelia.dir/edge.cpp.o.d -o CMakeFiles/Sibelia.dir/edge.cpp.o -c /<<PKGBUILDDIR>>/src/edge.cpp
[ 60%] Building CXX object CMakeFiles/Sibelia.dir/fasta.cpp.o
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/fasta.cpp.o -MF CMakeFiles/Sibelia.dir/fasta.cpp.o.d -o CMakeFiles/Sibelia.dir/fasta.cpp.o -c /<<PKGBUILDDIR>>/src/fasta.cpp
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/fasta.h:10,
                 from /<<PKGBUILDDIR>>/src/postprocessor.h:13,
                 from /<<PKGBUILDDIR>>/src/postprocessor.cpp:9:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/fasta.h:10,
                 from /<<PKGBUILDDIR>>/src/postprocessor.h:13,
                 from /<<PKGBUILDDIR>>/src/sibelia.cpp:8:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:10,
                 from /<<PKGBUILDDIR>>/src/blockfinder.h:10,
                 from /<<PKGBUILDDIR>>/src/bulgeremoval.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_algobase.h:65,
                 from /usr/include/c++/14/algorithm:60,
                 from /usr/include/seqan/align.h:53,
                 from /<<PKGBUILDDIR>>/src/postprocessor.h:10:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11,
                 from /<<PKGBUILDDIR>>/src/postprocessor.h:14:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/fasta.h:10,
                 from /<<PKGBUILDDIR>>/src/dnasequence.h:10,
                 from /<<PKGBUILDDIR>>/src/dnasequence.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp: In member function ‘void SyntenyFinder::Postprocessor::LocalAlignment(const std::string&, const std::string&, std::pair<long unsigned int, long unsigned int>&, std::pair<long unsigned int, long unsigned int>&)’:
/<<PKGBUILDDIR>>/src/postprocessor.cpp:259:33: error: ‘seqan’ is not a namespace-name
  259 |                 using namespace seqan;
      |                                 ^~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:260:25: error: ‘String’ does not name a type
  260 |                 typedef String<char>                            TSequence;      // sequence type
      |                         ^~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:261:25: error: ‘Align’ does not name a type
  261 |                 typedef Align<TSequence, ArrayGaps>     TAlign;         // align type
      |                         ^~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:262:25: error: ‘Row’ does not name a type
  262 |                 typedef Row<TAlign>::Type                       TRow;
      |                         ^~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:263:25: error: ‘Iterator’ does not name a type; did you mean ‘BLCIterator’?
  263 |                 typedef Iterator<TRow>::Type            TIterator;
      |                         ^~~~~~~~
      |                         BLCIterator
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /usr/include/tclap/SwitchArg.h:29,
                 from /usr/include/tclap/CmdLine.h:27,
                 from /<<PKGBUILDDIR>>/src/sibelia.cpp:7:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:264:25: error: ‘Position’ does not name a type
  264 |                 typedef Position<TAlign>::Type          TPosition;
      |                         ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11,
                 from /<<PKGBUILDDIR>>/src/postprocessor.h:14:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:266:17: error: ‘TSequence’ was not declared in this scope; did you mean ‘sequence1’?
  266 |                 TSequence seq1 = sequence1;
      |                 ^~~~~~~~~
      |                 sequence1
/<<PKGBUILDDIR>>/src/postprocessor.cpp:267:26: error: expected ‘;’ before ‘seq2’
  267 |                 TSequence seq2 = sequence2;
      |                          ^~~~~
      |                          ;
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:268:17: error: ‘TAlign’ was not declared in this scope
  268 |                 TAlign align;
      |                 ^~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:269:29: error: ‘align’ was not declared in this scope; did you mean ‘std::align’?
  269 |                 resize(rows(align), 2);
      |                             ^~~~~
      |                             std::align
In file included from /usr/include/c++/14/memory:74,
                 from /usr/include/seqan/basic/test_system.h:53,
                 from /usr/include/seqan/basic.h:65,
                 from /usr/include/seqan/align.h:55:
/usr/include/c++/14/bits/align.h:61:1: note: ‘std::align’ declared here
   61 | align(size_t __align, size_t __size, void*& __ptr, size_t& __space) noexcept
      | ^~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:269:24: error: ‘rows’ was not declared in this scope; did you mean ‘seqan2::rows’?
  269 |                 resize(rows(align), 2);
      |                        ^~~~
      |                        seqan2::rows
In file included from /usr/include/seqan/align.h:97:
/usr/include/seqan/align/align_base.h:341:1: note: ‘seqan2::rows’ declared here
  341 | rows(Align<TSource, TSpec> const & me)
      | ^~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:269:17: error: ‘resize’ was not declared in this scope; did you mean ‘seqan2::resize’?
  269 |                 resize(rows(align), 2);
      |                 ^~~~~~
      |                 seqan2::resize
In file included from /usr/include/seqan/align.h:146:
/usr/include/seqan/align/dp_matrix_sparse.h:95:1: note: ‘seqan2::resize’ declared here
   95 | resize(DPMatrix_<TValue, SparseDPMatrix, THost> & dpMatrix,
      | ^~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:270:30: error: ‘row’ was not declared in this scope; did you mean ‘seqan2::row’?
  270 |                 assignSource(row(align, 0), seq1);
      |                              ^~~
      |                              seqan2::row
/usr/include/seqan/align/align_base.h:372:1: note: ‘seqan2::row’ declared here
  372 | row(Align<TSource, TSpec> const & me,
      | ^~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:270:45: error: ‘seq1’ was not declared in this scope
  270 |                 assignSource(row(align, 0), seq1);
      |                                             ^~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:270:17: error: ‘assignSource’ was not declared in this scope; did you mean ‘seqan2::assignSource’?
  270 |                 assignSource(row(align, 0), seq1);
      |                 ^~~~~~~~~~~~
      |                 seqan2::assignSource
In file included from /usr/include/seqan/align.h:89:
/usr/include/seqan/align/gaps_anchor.h:672:1: note: ‘seqan2::assignSource’ declared here
  672 | assignSource(Gaps<TSequence, AnchorGaps<TGapAnchor> > & gaps, TSequence2 const & source)
      | ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:271:45: error: ‘seq2’ was not declared in this scope; did you mean ‘seqan2’?
  271 |                 assignSource(row(align, 1), seq2);
      |                                             ^~~~
      |                                             seqan2
/<<PKGBUILDDIR>>/src/postprocessor.cpp:272:39: error: ‘Score’ was not declared in this scope; did you mean ‘seqan2::Score’?
  272 |                 localAlignment(align, Score<int>(25, -75, -75));
      |                                       ^~~~~
      |                                       seqan2::Score
In file included from /usr/include/seqan/score.h:45,
                 from /usr/include/seqan/graph_align.h:45,
                 from /usr/include/seqan/align.h:59:
/usr/include/seqan/score/score_base.h:68:7: note: ‘seqan2::Score’ declared here
   68 | class Score;
      |       ^~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:272:45: error: expected primary-expression before ‘int’
  272 |                 localAlignment(align, Score<int>(25, -75, -75));
      |                                             ^~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:272:17: error: ‘localAlignment’ was not declared in this scope; did you mean ‘seqan2::localAlignment’?
  272 |                 localAlignment(align, Score<int>(25, -75, -75));
      |                 ^~~~~~~~~~~~~~
      |                 seqan2::localAlignment
In file included from /usr/include/seqan/align.h:209:
/usr/include/seqan/align/local_alignment_banded.h:306:21: note: ‘seqan2::localAlignment’ declared here
  306 | String<TScoreValue> localAlignment(StringSet<Align<TSequence, TAlignSpec> > & align,
      |                     ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:273:32: error: ‘clippedBeginPosition’ was not declared in this scope; did you mean ‘seqan2::clippedBeginPosition’?
  273 |                 coord1.first = clippedBeginPosition(row(align, 0));
      |                                ^~~~~~~~~~~~~~~~~~~~
      |                                seqan2::clippedBeginPosition
/usr/include/seqan/align/gaps_anchor.h:920:1: note: ‘seqan2::clippedBeginPosition’ declared here
  920 | clippedBeginPosition(Gaps<TSequence, AnchorGaps<TGapAnchors> > const & gaps)
      | ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/postprocessor.cpp:274:33: error: ‘clippedEndPosition’ was not declared in this scope; did you mean ‘seqan2::clippedEndPosition’?
  274 |                 coord1.second = clippedEndPosition(row(align, 0));
      |                                 ^~~~~~~~~~~~~~~~~~
      |                                 seqan2::clippedEndPosition
/usr/include/seqan/align/gaps_anchor.h:931:1: note: ‘seqan2::clippedEndPosition’ declared here
  931 | clippedEndPosition(Gaps<TSequence, AnchorGaps<TGapAnchors> > const & gaps)
      | ^~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/blockfinder.h:11,
                 from /<<PKGBUILDDIR>>/src/util.h:10,
                 from /<<PKGBUILDDIR>>/src/sibelia.cpp:9:
/<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   37 |                 std::auto_ptr<DNASequence> sequence_;
      |                      ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
                 from /usr/include/seqan/basic/test_system.h:53,
                 from /usr/include/seqan/basic.h:65,
                 from /usr/include/seqan/align.h:55,
                 from /<<PKGBUILDDIR>>/src/postprocessor.h:10:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   38 |                 std::auto_ptr<BifurcationStorage> bifStorage_;
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/sibelia.cpp: In function ‘int main(int, char**)’:
/<<PKGBUILDDIR>>/src/sibelia.cpp:239:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
  239 |                 std::auto_ptr<SyntenyFinder::BlockFinder> finder(inRAM.isSet() ? new SyntenyFinder::BlockFinder(chrList) : new SyntenyFinder::BlockFinder(chrList, tempDir));
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/blockfinder.h:11:
/<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   37 |                 std::auto_ptr<DNASequence> sequence_;
      |                      ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
                 from /<<PKGBUILDDIR>>/src/common.h:20:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   38 |                 std::auto_ptr<BifurcationStorage> bifStorage_;
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
[ 65%] Building CXX object CMakeFiles/Sibelia.dir/serialization.cpp.o
/usr/bin/c++  -I/<<PKGBUILDDIR>>/src/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -MD -MT CMakeFiles/Sibelia.dir/serialization.cpp.o -MF CMakeFiles/Sibelia.dir/serialization.cpp.o.d -o CMakeFiles/Sibelia.dir/serialization.cpp.o -c /<<PKGBUILDDIR>>/src/serialization.cpp
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:10,
                 from /<<PKGBUILDDIR>>/src/blockfinder.h:10,
                 from /<<PKGBUILDDIR>>/src/edge.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
make[3]: *** [CMakeFiles/Sibelia.dir/build.make:96: CMakeFiles/Sibelia.dir/postprocessor.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/fasta.h:10,
                 from /<<PKGBUILDDIR>>/src/fasta.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/blockfinder.h:11:
/<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   37 |                 std::auto_ptr<DNASequence> sequence_;
      |                      ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
                 from /<<PKGBUILDDIR>>/src/common.h:20:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   38 |                 std::auto_ptr<BifurcationStorage> bifStorage_;
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /usr/include/boost/bind/detail/requires_cxx11.hpp:9,
                 from /usr/include/boost/bind/bind.hpp:24,
                 from /usr/include/boost/bind.hpp:29,
                 from /<<PKGBUILDDIR>>/src/common.h:31,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:10,
                 from /<<PKGBUILDDIR>>/src/blockfinder.h:10,
                 from /<<PKGBUILDDIR>>/src/serialization.cpp:7:
/usr/include/boost/bind.hpp:36:1: note: ‘#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.’
   36 | BOOST_PRAGMA_MESSAGE(
      | ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/common.h:104:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
  104 |                 struct FancyIterator: public std::iterator<std::forward_iterator_tag, ReturnType>
      |                                                   ^~~~~~~~
In file included from /usr/include/c++/14/bits/stl_iterator_base_funcs.h:66,
                 from /usr/include/c++/14/string:47,
                 from /<<PKGBUILDDIR>>/src/common.h:12:
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/dnasequence.h:12,
                 from /<<PKGBUILDDIR>>/src/blockinstance.h:11:
/<<PKGBUILDDIR>>/src/unrolledlist.h:36:45: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   36 |                 class iterator: public std::iterator<std::bidirectional_iterator_tag, T>
      |                                             ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
/<<PKGBUILDDIR>>/src/dnasequence.h:51:51: warning: ‘template<class _Category, class _Tp, class _Distance, class _Pointer, class _Reference> struct std::iterator’ is deprecated [-Wdeprecated-declarations]
   51 |                 class StrandIterator: public std::iterator<std::bidirectional_iterator_tag, char, size_t>
      |                                                   ^~~~~~~~
/usr/include/c++/14/bits/stl_iterator_base_types.h:127:34: note: declared here
  127 |     struct _GLIBCXX17_DEPRECATED iterator
      |                                  ^~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/blockfinder.h:11:
/<<PKGBUILDDIR>>/src/indexedsequence.h:37:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   37 |                 std::auto_ptr<DNASequence> sequence_;
      |                      ^~~~~~~~
In file included from /usr/include/c++/14/memory:78,
                 from /<<PKGBUILDDIR>>/src/common.h:20:
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
/<<PKGBUILDDIR>>/src/indexedsequence.h:38:22: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
   38 |                 std::auto_ptr<BifurcationStorage> bifStorage_;
      |                      ^~~~~~~~
/usr/include/c++/14/bits/unique_ptr.h:59:28: note: declared here
   59 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[2]: *** [CMakeFiles/Makefile2:90: CMakeFiles/Sibelia.dir/all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
make[1]: *** [Makefile:159: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu'
dh_auto_build: error: cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2
make: *** [debian/rules:11: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-11-23T10:30:18Z

Finished
--------


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

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

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

Build Architecture: arm64
Build Type: binary
Build-Space: 48108
Build-Time: 12
Distribution: sid
Fail-Stage: build
Host Architecture: arm64
Install-Time: 31
Job: /tmp/debusine-fetch-exec-upload-qm6wlalt/sibelia_3.0.7+dfsg-3.dsc
Machine Architecture: arm64
Package: sibelia
Package-Time: 74
Source-Version: 3.0.7+dfsg-3
Space: 48108
Status: attempted
Version: 3.0.7+dfsg-3
--------------------------------------------------------------------------------
Finished at 2024-11-23T10:30:18Z
Build needed 00:01:14, 48108k disk space

Relations

Relation Direction Type Name
relates-to Source package sibelia_3.0.7+dfsg-3
relates-to Binary package seqan-apps-dbgsym_2.5.0~rc3+dfsg-1_arm64
relates-to Binary package seqan-apps_2.5.0~rc3+dfsg-1_arm64
relates-to Binary package libseqan2-dev_2.5.0~rc3+dfsg-1_all

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