sbuild (Debian sbuild) 0.85.9 (29 May 2024) on carme.larted.org.uk

+==============================================================================+
| mecat2 0.0+git20200428.f54c542+ds-4 (amd64)  Tue, 04 Jun 2024 15:32:28 +0000 |
+==============================================================================+

Package: mecat2
Version: 0.0+git20200428.f54c542+ds-4
Source Version: 0.0+git20200428.f54c542+ds-4
Distribution: perl-5.40-throwaway
Machine Architecture: amd64
Host Architecture: amd64
Build Architecture: amd64
Build Type: full

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/perl-5.40-amd64-debomatic-4580a6c3-dbef-48e0-a904-779598e12dca' with '<<CHROOT>>'

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


/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup mecat2_0.0+git20200428.f54c542+ds-4 perl-5.40-throwaway amd64
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I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup mecat2_0.0+git20200428.f54c542+ds-4 perl-5.40-throwaway amd64'.

Finished processing commands.
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I: NOTICE: Log filtering will replace 'build/mecat2-ErW23h/resolver-Ynutpa' with '<<RESOLVERDIR>>'

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| Update chroot                                                                |
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Get:1 file:/srv/reprepro perl-5.40 InRelease [3039 B]
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Get:2 file:/srv/reprepro perl-5.40/main amd64 Packages [598 kB]
Get:3 http://localhost:3142/debian unstable InRelease [198 kB]
Get:4 http://localhost:3142/debian sid InRelease [198 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [81.5 kB]
Get:7 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 Packages T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [81.5 kB]
Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [53.9 kB]
Get:8 http://localhost:3142/debian sid/main Sources T-2024-06-04-1405.10-F-2024-06-03-0205.12.pdiff [53.9 kB]
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Reading package lists...
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Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
  bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 login passwd util-linux
8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 3414 kB of archives.
After this operation, 57.3 kB disk space will be freed.
Get:1 http://localhost:3142/debian unstable/main amd64 bsdutils amd64 1:2.40.1-8 [104 kB]
Get:2 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.13+dfsg1-5 [590 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 libsmartcols1 amd64 2.40.1-8 [137 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 libuuid1 amd64 2.40.1-8 [34.7 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 libblkid1 amd64 2.40.1-8 [166 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 libmount1 amd64 2.40.1-8 [197 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 util-linux amd64 2.40.1-8 [1210 kB]
Get:8 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.13+dfsg1-5 [974 kB]
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Processing triggers for libc-bin (2.38-12) ...

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| Fetch source files                                                           |
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Local sources
-------------

/srv/debomatic/incoming/mecat2_0.0+git20200428.f54c542+ds-4.dsc exists in /srv/debomatic/incoming; copying to chroot
I: NOTICE: Log filtering will replace 'build/mecat2-ErW23h/mecat2-0.0+git20200428.f54c542+ds' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/mecat2-ErW23h' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), zlib1g-dev, perl, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), zlib1g-dev, perl, 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 [635 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [667 B]
Fetched 1911 B in 0s (0 B/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64
  libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc
  libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 m4 man-db po-debconf
  sensible-utils zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc
  libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl
Recommended packages:
  curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-strip-nondeterminism dwz fakeroot file gettext gettext-base
  groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64
  libfakeroot libfile-stripnondeterminism-perl libicu72 libmagic-mgc
  libmagic1t64 libpipeline1 libtool libuchardet0 libxml2 m4 man-db po-debconf
  sbuild-build-depends-main-dummy sensible-utils zlib1g-dev
0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.0 MB of archives.
After this operation, 75.2 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [892 B]
Get:2 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.22 [22.4 kB]
Get:3 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB]
Get:4 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB]
Get:5 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3 [42.9 kB]
Get:6 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.21-14+b1 [161 kB]
Get:7 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b1 [68.8 kB]
Get:8 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-4 [1180 kB]
Get:9 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.1-8 [96.0 kB]
Get:10 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.7-2 [38.0 kB]
Get:11 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.12.1-1 [1411 kB]
Get:12 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get:13 http://localhost:3142/debian unstable/main amd64 autoconf all 2.71-3 [332 kB]
Get:14 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:15 http://localhost:3142/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:16 http://localhost:3142/debian unstable/main amd64 autopoint all 0.21-14 [496 kB]
Get:17 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.15.3 [88.0 kB]
Get:18 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-7 [517 kB]
Get:19 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:20 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:21 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB]
Get:22 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B]
Get:23 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.191-1+b1 [189 kB]
Get:24 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB]
Get:25 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB]
Get:26 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg-3 [670 kB]
Get:27 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.21-14+b1 [1301 kB]
Get:28 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:29 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:30 http://localhost:3142/debian unstable/main amd64 debhelper all 13.15.3 [901 kB]
Get:31 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.34-1 [28.9 kB]
Get:32 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.34-1 [74.0 kB]
Get:33 http://localhost:3142/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1 [919 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up libpipeline1:amd64 (1.5.7-2) ...
Setting up libicu72:amd64 (72.1-4+b1) ...
Setting up bsdextrautils (2.40.1-8) ...
Setting up libmagic-mgc (1:5.45-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.15.3) ...
Setting up libmagic1t64:amd64 (1:5.45-3) ...
Setting up gettext-base (0.21-14+b1) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-3) ...
Setting up libfakeroot:amd64 (1.34-1) ...
Setting up libelf1t64:amd64 (0.191-1+b1) ...
Setting up fakeroot (1.34-1) ...
update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode
Setting up autotools-dev (20220109.1) ...
Setting up autopoint (0.21-14) ...
Setting up autoconf (2.71-3) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1) ...
Setting up dwz (0.15-1+b1) ...
Setting up sensible-utils (0.0.22) ...
Setting up libuchardet0:amd64 (0.0.8-1+b1) ...
Setting up libxml2:amd64 (2.12.7+dfsg-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 libfile-stripnondeterminism-perl (1.14.0-1) ...
Setting up gettext (0.21-14+b1) ...
Setting up libtool (2.4.7-7) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.14.0-1) ...
Setting up groff-base (1.23.0-4) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up man-db (2.12.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up debhelper (13.15.3) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.38-12) ...

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

Arch check ok (amd64 included in any-amd64)

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

Kernel: Linux 6.1.0-21-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.90-1 (2024-05-03) amd64 (x86_64)
Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-25 gcc-13_13.2.0-25 libc6-dev_2.38-12 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 linux-libc-dev_6.8.12-1
Package versions: adduser_3.137 apt_2.9.4 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.2 base-passwd_3.6.3 bash_5.2.21-2+b1 binutils_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40.1-8 bsdutils_1:2.40.1-8 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-25 cpp-13-x86-64-linux-gnu_13.2.0-25 cpp-x86-64-linux-gnu_4:13.2.0-7 dash_0.5.12-8 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dirmngr_2.2.43-7 dpkg_1.22.6 dpkg-dev_1.22.6 dwz_0.15-1+b1 eatmydata_131-2 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-6 g++_4:13.2.0-7 g++-13_13.2.0-25 g++-13-x86-64-linux-gnu_13.2.0-25 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-25 gcc-13-base_13.2.0-25 gcc-13-x86-64-linux-gnu_13.2.0-25 gcc-14-base_14.1.0-1 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gnupg_2.2.43-7 gnupg-l10n_2.2.43-7 gnupg-utils_2.2.43-7 gpg_2.2.43-7 gpg-agent_2.2.43-7 gpg-wks-client_2.2.43-7 gpgconf_2.2.43-7 gpgsm_2.2.43-7 gpgv_2.2.43-7 grep_3.11-4 groff-base_1.23.0-4 gzip_1.12-1.1 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2 libapt-pkg6.0t64_2.9.4 libarchive-zip-perl_1.68-1 libasan8_14.1.0-1 libassuan0_2.5.6-1+b1 libatomic1_14.1.0-1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblkid1_2.40.1-8 libbz2-1.0_1.0.8-5.1 libc-bin_2.38-12 libc-dev-bin_2.38-12 libc-l10n_2.38-12 libc6_2.38-12 libc6-dev_2.38-12 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14.1.0-1 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.272 libdebhelper-perl_13.15.3 libdpkg-perl_1.22.6 libeatmydata1_131-2 libelf1t64_0.191-1+b1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.0-1 libgcc-13-dev_13.2.0-25 libgcc-s1_14.1.0-1 libgcrypt20_1.10.3-3 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-4 libgomp1_14.1.0-1 libgpg-error0_1.49-2 libgprofng0_2.42-4 libhogweed6t64_3.9.1-2.2 libhwasan0_14.1.0-1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libisl23_0.26-3+b2 libitm1_14.1.0-1 libjansson4_2.14-2+b2 libksba8_1.6.6-1 libldap-2.5-0_2.5.17+dfsg-1+b1 liblsan0_14.1.0-1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40.1-8 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.5-2 libnettle8t64_3.9.1-2.2 libnpth0t64_1.6-3.1 libp11-kit0_0.25.3-5 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.0~rc1-1 libpipeline1_1.5.7-2 libquadmath0_14.1.0-1 libreadline8t64_8.2-4 libsasl2-2_2.1.28+dfsg1-6 libsasl2-modules-db_2.1.28+dfsg1-6 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsemanage-common_3.5-1 libsemanage2_3.5-1+b3 libsepol2_3.5-2+b1 libsframe1_2.42-4 libsmartcols1_2.40.1-8 libsqlite3-0_3.46.0-1 libssl3t64_3.2.1-3 libstdc++-13-dev_13.2.0-25 libstdc++6_14.1.0-1 libsystemd0_256~rc3-7 libtasn1-6_4.19.0-3+b2 libtinfo6_6.5-2 libtool_2.4.7-7 libtsan2_14.1.0-1 libubsan1_14.1.0-1 libuchardet0_0.0.8-1+b1 libudev1_256~rc3-7 libunistring5_1.2-1 libuuid1_2.40.1-8 libxml2_2.12.7+dfsg-3 libxxhash0_0.8.2-2+b1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.8.12-1 locales-all_2.38-12 login_1:4.13+dfsg1-5 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 ncurses-base_6.5-2 ncurses-bin_6.5-2 passwd_1:4.13+dfsg1-5 patch_2.7.6-7 perl_5.40.0~rc1-1 perl-base_5.40.0~rc1-1 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.0~rc1-1 pinentry-curses_1.2.1-3+b2 po-debconf_1.0.21+nmu1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 tar_1.35+dfsg-3 usr-is-merged_39 util-linux_2.40.1-8 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg+really1.3.1-1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1

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


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

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 3.0 (quilt)
Source: mecat2
Binary: mecat2
Architecture: any-amd64
Version: 0.0+git20200428.f54c542+ds-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Shayan Doust <hello@shayandoust.me>
Homepage: https://github.com/xiaochuanle/MECAT2
Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/mecat2
Vcs-Git: https://salsa.debian.org/med-team/mecat2.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), zlib1g-dev, perl
Package-List:
 mecat2 deb science optional arch=any-amd64,x32
Checksums-Sha1:
 3422fa4cc700ac60aaec8050b8a98612b444b678 381084 mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz
 8b283121f74d8922811d74c432b6ec2fecc24e86 338661480 mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz
Checksums-Sha256:
 32f66c44306f1ebffed4ef3b5ba26041387d16561627ff93aa69bf6ee1107e31 381084 mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz
 e00dea2e6659c6dee053a91d67c5dce92a8ff59fc023d029443b7998ec083ab0 338661480 mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz
Files:
 1e944b07acb5474e4da65cb10b829ec0 381084 mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz
 449343e86843c0b8f229b939ba98b1b5 338661480 mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz

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gpgv: Signature made Tue Nov  7 07:57:44 2023 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./mecat2_0.0+git20200428.f54c542+ds-4.dsc: no acceptable signature found
dpkg-source: info: extracting mecat2 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz
dpkg-source: info: unpacking mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying modify_makefiles.patch
dpkg-source: info: applying fix-gcc13-ftbfs.patch

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

Sufficient free space for build

+------------------------------------------------------------------------------+
| Starting Timed Build Commands                                                |
+------------------------------------------------------------------------------+


/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network mecat2_0.0+git20200428.f54c542+ds-4 perl-5.40-throwaway amd64
------------------------------------------------------------------------------------------------------------------------------------


I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network mecat2_0.0+git20200428.f54c542+ds-4 perl-5.40-throwaway amd64'.

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

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

APT_CONFIG=/var/lib/sbuild/apt.conf
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LANGUAGE=en_GB:en
LC_ALL=C.UTF-8
LD_LIBRARY_PATH=/usr/lib/libeatmydata
LD_PRELOAD=libeatmydata.so
LOGNAME=debomatic
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic
SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic
SCHROOT_COMMAND=env
SCHROOT_GID=110
SCHROOT_GROUP=sbuild
SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-4580a6c3-dbef-48e0-a904-779598e12dca
SCHROOT_UID=1002
SCHROOT_USER=debomatic
SHELL=/bin/sh
USER=debomatic

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

Command: dpkg-buildpackage --sanitize-env -us -uc -rfakeroot -Zxz
dpkg-buildpackage: info: source package mecat2
dpkg-buildpackage: info: source version 0.0+git20200428.f54c542+ds-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
 dpkg-source -Zxz --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   dh_auto_clean
	make -j2 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
Building for 'Linux' '6.1.0-21-amd64' as 'amd64'
Makefile:401: warning: overriding recipe for target '../Linux-amd64/bin/mecat2cns'
Makefile:401: warning: ignoring old recipe for target '../Linux-amd64/bin/mecat2cns'
Makefile:418: warning: overriding recipe for target 'clean_mecat2cns'
Makefile:418: warning: ignoring old recipe for target 'clean_mecat2cns'
rm -f ../Linux-amd64/bin/libhbn.a ../Linux-amd64/obj/libhbn.a/corelib/build_db.[doP] ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.[doP] ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.[doP] ../Linux-amd64/obj/libhbn.a/corelib/db_format.[doP] ../Linux-amd64/obj/libhbn.a/corelib/fasta.[doP] ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.[doP] ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.[doP] ../Linux-amd64/obj/libhbn.a/corelib/kstring.[doP] ../Linux-amd64/obj/libhbn.a/corelib/line_reader.[doP] ../Linux-amd64/obj/libhbn.a/corelib/m4_record.[doP] ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.[doP] ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.[doP] ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seqdb.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.[doP] ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.[doP] ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.[doP] ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.[doP] ../Linux-amd64/obj/libhbn.a/algo/chain_dp.[doP] ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.[doP] ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.[doP] ../Linux-amd64/obj/libhbn.a/algo/kalloc.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.[doP] ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.[doP] ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.[doP] ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.[doP] ../Linux-amd64/obj/libhbn.a/algo/word_finder.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.[doP] ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.[doP]
rm -f ../Linux-amd64/bin/mecat2pcan ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.[doP]
rm -f ../Linux-amd64/bin/mecat2map ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_options.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.[doP] ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.[doP] ../Linux-amd64/obj/mecat2map/app/map/main.[doP] ../Linux-amd64/obj/mecat2map/app/map/mecat_results.[doP]
rm -f ../Linux-amd64/bin/mecat2cns ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.[doP] ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.[doP]
rm -f ../Linux-amd64/bin/mecat2viewdb ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.[doP]
rm -f ../Linux-amd64/bin/mecat2lcr ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.[doP] ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.[doP]
rm -f ../Linux-amd64/bin/mecat2splitreads ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.[doP] ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.[doP]
rm -f ../Linux-amd64/bin/mecat2trimbases ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.[doP]
rm -f ../Linux-amd64/bin/mecat2pm4 ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.[doP]
rm -f ../Linux-amd64/bin/mecat2extseqs ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.[doP]
rm -f ../Linux-amd64/bin/libfsa.a ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/logger.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/utility.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.[doP] ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.[doP]
rm -f ../Linux-amd64/bin/fsa_ol_filter ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.[doP]
rm -f ../Linux-amd64/bin/fsa_assemble ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.[doP] ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.[doP]
rm -f ../Linux-amd64/bin/fsa_ctg_bridge ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.[doP] ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.[doP]
rm -f ../Linux-amd64/bin/fsa_rd_stat ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.[doP] ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.[doP]
rm -f ../Linux-amd64/bin/mecat.pl
rm -f ../Linux-amd64/bin/mecat.sh
rm -f 
rm -f  ../Linux-amd64/bin/Plgd/Grid.pm  ../Linux-amd64/bin/Plgd/GridLsf.pm  ../Linux-amd64/bin/Plgd/GridPbs.pm  ../Linux-amd64/bin/Plgd/GridSge.pm  ../Linux-amd64/bin/Plgd/GridSlurm.pm  ../Linux-amd64/bin/Plgd/Project.pm  ../Linux-amd64/bin/Plgd/Script.pm  ../Linux-amd64/bin/Plgd/Utils.pm
rm -rf ../Linux-amd64/bin/Plgd
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
 dpkg-source -Zxz -b .
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building mecat2 using existing ./mecat2_0.0+git20200428.f54c542+ds.orig.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: building mecat2 in mecat2_0.0+git20200428.f54c542+ds-4.debian.tar.xz
dpkg-source: info: building mecat2 in mecat2_0.0+git20200428.f54c542+ds-4.dsc
 debian/rules binary
dh binary
   dh_update_autotools_config
   dh_autoreconf
   dh_auto_configure
   dh_auto_build
	make -j2 "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<PKGBUILDDIR>>'
cd src && make
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: warning: jobserver unavailable: using -j1.  Add '+' to parent make rule.
Building for 'Linux' '6.1.0-21-amd64' as 'amd64'
Makefile:401: warning: overriding recipe for target '../Linux-amd64/bin/mecat2cns'
Makefile:401: warning: ignoring old recipe for target '../Linux-amd64/bin/mecat2cns'
Makefile:418: warning: overriding recipe for target 'clean_mecat2cns'
Makefile:418: warning: ignoring old recipe for target 'clean_mecat2cns'
cp -pf pipeline/mecat.pl ../Linux-amd64/bin/mecat.pl
chmod +x ../Linux-amd64/bin/mecat.pl
cp -pf pipeline/mecat.sh ../Linux-amd64/bin/mecat.sh
chmod +x ../Linux-amd64/bin/mecat.sh
cp -pf  pipeline/Plgd/Grid.pm ../Linux-amd64/bin/Plgd/Grid.pm
cp -pf  pipeline/Plgd/GridLsf.pm ../Linux-amd64/bin/Plgd/GridLsf.pm
cp -pf  pipeline/Plgd/GridPbs.pm ../Linux-amd64/bin/Plgd/GridPbs.pm
cp -pf  pipeline/Plgd/GridSge.pm ../Linux-amd64/bin/Plgd/GridSge.pm
cp -pf  pipeline/Plgd/GridSlurm.pm ../Linux-amd64/bin/Plgd/GridSlurm.pm
cp -pf  pipeline/Plgd/Project.pm ../Linux-amd64/bin/Plgd/Project.pm
cp -pf  pipeline/Plgd/Script.pm ../Linux-amd64/bin/Plgd/Script.pm
cp -pf  pipeline/Plgd/Utils.pm ../Linux-amd64/bin/Plgd/Utils.pm
cc -o ../Linux-amd64/obj/libhbn.a/corelib/build_db.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/build_db.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/cmd_arg.c
g++ -o ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/cstr_util.cpp
cc -o ../Linux-amd64/obj/libhbn.a/corelib/db_format.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/db_format.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/fasta.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/fasta.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/gapped_candidate.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_aux.c
corelib/hbn_aux.c: In function ‘hbn_get_cpu_count’:
corelib/hbn_aux.c:357:9: warning: unused variable ‘allCPUNum_’ [-Wunused-variable]
  357 |     int allCPUNum_    = sysconf(_SC_NPROCESSORS_CONF);
      |         ^~~~~~~~~~
cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_format.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_hit.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/hbn_package_version.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/kstring.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/kstring.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/line_reader.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/m4_record.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/name2id_map.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/partition_aux.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/raw_reads.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seqdb_summary.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seqdb.c
cc -o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/seq_tag.c
corelib/seq_tag.c:480:1: warning: ‘examine_ovlp_quality_perfect’ defined but not used [-Wunused-function]
  480 | examine_ovlp_quality_perfect(int qoff,
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
corelib/seq_tag.c:9:12: warning: ‘CircularSeq’ defined but not used [-Wunused-variable]
    9 | static int CircularSeq = 0;
      |            ^~~~~~~~~~~
corelib/seq_tag.c:7:12: warning: ‘RepeatSeq’ defined but not used [-Wunused-variable]
    7 | static int RepeatSeq = 0;
      |            ^~~~~~~~~
g++ -o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/seq_tag_report.cpp
cc -o ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp corelib/small_object_alloc.c
g++ -o ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp corelib/string2hsp.cpp
cc -o ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/chain_dp.c
algo/chain_dp.c: In function ‘find_best_kmer_match’:
algo/chain_dp.c:164:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  164 |     memset(t, 0, sizeof(int) * n);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
algo/chain_dp.c: In function ‘chaining_find_candidates’:
algo/chain_dp.c:257:5: warning: ‘memset’ specified bound between 18446744065119617024 and 18446744073709551612 exceeds maximum object size 9223372036854775807 [-Wstringop-overflow=]
  257 |     memset(t, 0, sizeof(int) * n);
      |     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp algo/diff_gapalign.cpp
algo/diff_gapalign.cpp:375:1: warning: ‘void dump_subseq(const u8*, int)’ defined but not used [-Wunused-function]
  375 | dump_subseq(const u8* seq, int len)
      | ^~~~~~~~~~~
cc -o ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hash_list_bucket_sort.c
cc -o ../Linux-amd64/obj/libhbn.a/algo/kalloc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/kalloc.c
cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_extd2_sse.c
cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_extz2_sse.c
cc -o ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/ksw2_wrapper.c
cc -o ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hbn_lookup_table.c
cc -o ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/hbn_traceback_aux.c
cc -o ../Linux-amd64/obj/libhbn.a/algo/word_finder.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp algo/word_finder.c
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/c_ncbi_blast_aux.c
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/ncbi_blast_aux.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/blast_args.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/cmdline_flags.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/format_flags.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_allow.cpp
ncbi_blast/cmdline_args/ncbiargs_allow.cpp:85:15: warning: ‘std::string ncbi::s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass)’ defined but not used [-Wunused-function]
   85 | static string s_GetSymbolClass(CArgAllow_Symbols::ESymbolClass symbol_class)
      |               ^~~~~~~~~~~~~~~~
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_desc.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/cmdline_args/ncbiargs_types.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr_util.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/ncbistr.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/str_cmp.cpp
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/numeric_str_interconv.cpp
ncbi_blast/str_util/numeric_str_interconv.cpp: In function ‘ncbi::SIZE_TYPE ns_hbnstr::DoubleToString_Ecvt(double, unsigned int, char*, ncbi::SIZE_TYPE, int*, int*)’:
ncbi_blast/str_util/numeric_str_interconv.cpp:2175:20: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying between 0 and 15 bytes from a string of length 31 [-Wstringop-truncation]
 2175 |             strncpy(buffer,digits,digits_len);
      |             ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/str_util/str_util.cpp
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_encoding.c
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_hits.c
ncbi_blast/setup/blast_hits.c:3897:1: warning: ‘s_TrimResultsByTotalHSPLimitEx’ defined but not used [-Wunused-function]
 3897 | s_TrimResultsByTotalHSPLimitEx(BlastHSPResults* results,
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbi_blast/setup/blast_hits.c:3815:1: warning: ‘s_TrimResultsByTotalHSPLimit’ defined but not used [-Wunused-function]
 3815 | s_TrimResultsByTotalHSPLimit(BlastHSPResults* results, Uint4 total_hsp_limit)
      | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
ncbi_blast/setup/blast_hits.c:3580:12: warning: ‘s_SortHspWrapRawScore’ defined but not used [-Wunused-function]
 3580 | static int s_SortHspWrapRawScore(const void *x, const void *y)
      |            ^~~~~~~~~~~~~~~~~~~~~
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_message.c
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_options.c
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_stat.c
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_parameters.c
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_program.c
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/setup/blast_types.cpp
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/boost_erf.c
g++ -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp ncbi_blast/setup/hsp2string.cpp
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/ncbi_math.c
In file included from ncbi_blast/setup/ncbi_math.c:498:
ncbi_blast/setup/ncbi_erf.c: In function ‘s_IEEE754_Exp’:
ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   40 | #define __LO(x) *(int*)&x
      |                  ^
ncbi_blast/setup/ncbi_erf.c:140:34: note: in expansion of macro ‘__LO’
  140 |                 if(((hx&0xfffff)|__LO(x))!=0)
      |                                  ^~~~
ncbi_blast/setup/ncbi_erf.c: In function ‘BLAST_Erf’:
ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   40 | #define __LO(x) *(int*)&x
      |                  ^
ncbi_blast/setup/ncbi_erf.c:401:9: note: in expansion of macro ‘__LO’
  401 |         __LO(z) = 0;
      |         ^~~~
ncbi_blast/setup/ncbi_erf.c: In function ‘BLAST_ErfC’:
ncbi_blast/setup/ncbi_erf.c:40:18: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   40 | #define __LO(x) *(int*)&x
      |                  ^
ncbi_blast/setup/ncbi_erf.c:462:13: note: in expansion of macro ‘__LO’
  462 |             __LO(z)  = 0;
      |             ^~~~
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_query_info.c
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/blast_sequence_blk.c
cc -o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp ncbi_blast/setup/gapinfo.c
ar rv ../Linux-amd64/bin/libhbn.a ../Linux-amd64/obj/libhbn.a/corelib/build_db.o ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o ../Linux-amd64/obj/libhbn.a/corelib/db_format.o ../Linux-amd64/obj/libhbn.a/corelib/fasta.o ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o ../Linux-amd64/obj/libhbn.a/corelib/kstring.o ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o ../Linux-amd64/obj/libhbn.a/algo/kalloc.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o ../Linux-amd64/obj/libhbn.a/algo/word_finder.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o
ar: creating ../Linux-amd64/bin/libhbn.a
a - ../Linux-amd64/obj/libhbn.a/corelib/build_db.o
a - ../Linux-amd64/obj/libhbn.a/corelib/cmd_arg.o
a - ../Linux-amd64/obj/libhbn.a/corelib/cstr_util.o
a - ../Linux-amd64/obj/libhbn.a/corelib/db_format.o
a - ../Linux-amd64/obj/libhbn.a/corelib/fasta.o
a - ../Linux-amd64/obj/libhbn.a/corelib/gapped_candidate.o
a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_aux.o
a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_format.o
a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_hit.o
a - ../Linux-amd64/obj/libhbn.a/corelib/hbn_package_version.o
a - ../Linux-amd64/obj/libhbn.a/corelib/kstring.o
a - ../Linux-amd64/obj/libhbn.a/corelib/line_reader.o
a - ../Linux-amd64/obj/libhbn.a/corelib/m4_record.o
a - ../Linux-amd64/obj/libhbn.a/corelib/name2id_map.o
a - ../Linux-amd64/obj/libhbn.a/corelib/partition_aux.o
a - ../Linux-amd64/obj/libhbn.a/corelib/raw_reads.o
a - ../Linux-amd64/obj/libhbn.a/corelib/seqdb_summary.o
a - ../Linux-amd64/obj/libhbn.a/corelib/seqdb.o
a - ../Linux-amd64/obj/libhbn.a/corelib/seq_tag.o
a - ../Linux-amd64/obj/libhbn.a/corelib/seq_tag_report.o
a - ../Linux-amd64/obj/libhbn.a/corelib/small_object_alloc.o
a - ../Linux-amd64/obj/libhbn.a/corelib/string2hsp.o
a - ../Linux-amd64/obj/libhbn.a/algo/chain_dp.o
a - ../Linux-amd64/obj/libhbn.a/algo/diff_gapalign.o
a - ../Linux-amd64/obj/libhbn.a/algo/hash_list_bucket_sort.o
a - ../Linux-amd64/obj/libhbn.a/algo/kalloc.o
a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_extd2_sse.o
a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_extz2_sse.o
a - ../Linux-amd64/obj/libhbn.a/algo/ksw2_wrapper.o
a - ../Linux-amd64/obj/libhbn.a/algo/hbn_lookup_table.o
a - ../Linux-amd64/obj/libhbn.a/algo/hbn_traceback_aux.o
a - ../Linux-amd64/obj/libhbn.a/algo/word_finder.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/c_ncbi_blast_aux.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/ncbi_blast_aux.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/blast_args.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/cmdline_flags.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/format_flags.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_allow.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_desc.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/cmdline_args/ncbiargs_types.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr_util.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/ncbistr.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_cmp.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/numeric_str_interconv.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/str_util/str_util.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_encoding.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_hits.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_message.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_options.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_stat.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_parameters.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_program.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_types.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/boost_erf.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/hsp2string.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/ncbi_math.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_query_info.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/blast_sequence_blk.o
a - ../Linux-amd64/obj/libhbn.a/ncbi_blast/setup/gapinfo.o
cc -o ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2pcan app/mecat2pcan/pcan.c
cc -o ../Linux-amd64/bin/mecat2pcan -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2pcan/app/mecat2pcan/pcan.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
g++ -o ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/map app/map/cmdline_args.cpp
app/map/cmdline_args.cpp:74:20: warning: ‘ncbi::kGroupExtension’ defined but not used [-Wunused-variable]
   74 | static const char* kGroupExtension = "Extension options";
      |                    ^~~~~~~~~~~~~~~
cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_align_one_volume.c
cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_build_seqdb.c
cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_extend_subseq_hit.c
cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_find_subseq_hit.c
In function ‘group_subject_init_hits’,
    inlined from ‘find_candidate_subject_subseqs’ at app/map/hbn_find_subseq_hit.c:151:22:
app/map/hbn_find_subseq_hit.c:39:51: warning: argument 1 range [18446743953450467328, 18446744073709551560] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=]
   39 |     HbnInitHit* tmp_init_hit_array = (HbnInitHit*)malloc(sizeof(HbnInitHit) * init_hit_count);
      |                                                   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from app/map/../../ncbi_blast/setup/../../corelib/kstring.h:29,
                 from app/map/../../ncbi_blast/setup/../../corelib/hbn_aux.h:11,
                 from app/map/../../ncbi_blast/setup/../c_ncbi_blast_aux.h:4,
                 from app/map/../../ncbi_blast/setup/blast_message.h:40,
                 from app/map/../../ncbi_blast/setup/blast_options.h:46,
                 from app/map/hbn_options.h:4,
                 from app/map/hbn_find_subseq_hit.h:4,
                 from app/map/hbn_find_subseq_hit.c:1:
/usr/include/stdlib.h: In function ‘find_candidate_subject_subseqs’:
/usr/include/stdlib.h:672:14: note: in a call to allocation function ‘malloc’ declared here
  672 | extern void *malloc (size_t __size) __THROW __attribute_malloc__
      |              ^~~~~~
cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_job_control.c
cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_options.c
cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_subseq_hit.c
cc -o ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/hbn_task_struct.c
cc -o ../Linux-amd64/obj/mecat2map/app/map/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/main.c
cc -o ../Linux-amd64/obj/mecat2map/app/map/mecat_results.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/map app/map/mecat_results.c
g++ -o ../Linux-amd64/bin/mecat2map -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2map/app/map/cmdline_args.o ../Linux-amd64/obj/mecat2map/app/map/hbn_align_one_volume.o ../Linux-amd64/obj/mecat2map/app/map/hbn_build_seqdb.o ../Linux-amd64/obj/mecat2map/app/map/hbn_extend_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_find_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_job_control.o ../Linux-amd64/obj/mecat2map/app/map/hbn_options.o ../Linux-amd64/obj/mecat2map/app/map/hbn_subseq_hit.o ../Linux-amd64/obj/mecat2map/app/map/hbn_task_struct.o ../Linux-amd64/obj/mecat2map/app/map/main.o ../Linux-amd64/obj/mecat2map/app/map/mecat_results.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
g++ -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cmdline_args.cpp
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_aux.c
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_one_part.c
g++ -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_one_read.cpp
app/mecat2cns/cns_one_read.cpp: In function ‘BOOL meap_consensus_one_segment(FCCnsData*, int*, int*, int, int, kstring_t*)’:
app/mecat2cns/cns_one_read.cpp:34:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare]
   34 |     if (ks_size(*cns_seq) < min_size) return FALSE;
In file included from app/mecat2cns/cns_one_read.h:4,
                 from app/mecat2cns/cns_one_read.cpp:1:
app/mecat2cns/cns_one_read.cpp: In function ‘void consensus_one_read(CnsThreadData*, int)’:
app/mecat2cns/cns_one_read.cpp:242:32: warning: comparison of integer expressions of different signedness: ‘const int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  242 |         hbn_assert(read_length == kv_size(*fwd_read_v));
app/mecat2cns/../../corelib/hbn_aux.h:115:15: note: in definition of macro ‘__hbn_assert’
  115 |         if (!(expr)) { \
      |               ^~~~
app/mecat2cns/cns_one_read.cpp:242:9: note: in expansion of macro ‘hbn_assert’
  242 |         hbn_assert(read_length == kv_size(*fwd_read_v));
      |         ^~~~~~~~~~
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/cns_options.c
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns_align_tag.c
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns_aux.c
app/mecat2cns/fccns_aux.c: In function ‘consensus_backbone_segment’:
app/mecat2cns/fccns_aux.c:137:9: warning: variable ‘g_best_ck’ set but not used [-Wunused-but-set-variable]
  137 |     int g_best_ck = 0;
      |         ^~~~~~~~~
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/fccns.c
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/hbn_task_struct.c
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/main.c
cc -o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -I-Iapp/mecat2cns app/mecat2cns/raw_reads_reader.c
g++ -o ../Linux-amd64/bin/mecat2cns -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cmdline_args.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_aux.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_part.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_one_read.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/cns_options.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_align_tag.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns_aux.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/fccns.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/hbn_task_struct.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/main.o ../Linux-amd64/obj/mecat2cns/app/mecat2cns/raw_reads_reader.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
cc -o ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/hbndb app/hbndb/viewhbndb.c
cc -o ../Linux-amd64/bin/mecat2viewdb -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2viewdb/app/hbndb/viewhbndb.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
g++ -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/cmdline_args.cpp
cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/largest_cover_range.c
cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/1_largest_cover_range/main.c
cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/common/range_list.c
cc -o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/1_largest_cover_range app/mecat2trim/common/m4_aux.c
g++ -o ../Linux-amd64/bin/mecat2lcr -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/cmdline_args.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/largest_cover_range.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/1_largest_cover_range/main.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/range_list.o ../Linux-amd64/obj/mecat2lcr/app/mecat2trim/common/m4_aux.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
g++ -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/cmdline_args.cpp
cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/main.c
cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/2_split_reads/split_reads.c
cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/range_list.c
cc -o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/2_split_reads app/mecat2trim/common/m4_aux.c
g++ -o ../Linux-amd64/bin/mecat2splitreads -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/cmdline_args.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/main.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/2_split_reads/split_reads.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/range_list.o ../Linux-amd64/obj/mecat2splitreads/app/mecat2trim/common/m4_aux.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
cc -o ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2trim/3_trim_bases app/mecat2trim/3_trim_bases/main.c
cc -o ../Linux-amd64/bin/mecat2trimbases -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2trimbases/app/mecat2trim/3_trim_bases/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
cc -o ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2pm4 app/mecat2pm4/main.c
cc -o ../Linux-amd64/bin/mecat2pm4 -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2pm4/app/mecat2pm4/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
cc -o ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/mecat2extseqs -Iapp/mecat2extseqs/libboost app/mecat2extseqs/main.c
cc -o ../Linux-amd64/bin/mecat2extseqs -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/mecat2extseqs/app/mecat2extseqs/main.o -lhbn -pthread -lm -lz -lstdc++ -fopenmp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/argument_parser.cpp
cc -o ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=gnu99 -DNDEBUG -fopenmp -Iapp/fsa app/fsa/getopt.c
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/logger.cpp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap.cpp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/read_store.cpp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/sequence.cpp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/utility.cpp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fasta_reader.cpp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fastq_reader.cpp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_store.cpp
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/simple_align.cpp
app/fsa/simple_align.cpp: In member function ‘SimpleAlign::Result SimpleAlign::Align(const std::string&, const std::string&, int, bool)’:
app/fsa/simple_align.cpp:153:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  153 |             if ( node.x + node.len  >= query.size() || node.y + node.len  >= target_.size()) {
      |                  ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
app/fsa/simple_align.cpp:153:75: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  153 |             if ( node.x + node.len  >= query.size() || node.y + node.len  >= target_.size()) {
      |                                                        ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_filter.cpp
app/fsa/overlap_filter.cpp: In member function ‘void OverlapFilter::FilterLocalStep(Seq::Id, const std::unordered_map<int, const Overlap*>&)’:
app/fsa/overlap_filter.cpp:413:18: warning: unused variable ‘loc’ [-Wunused-variable]
  413 |             auto loc = o.Location(max_overhang_);
      |                  ^~~
app/fsa/overlap_filter.cpp:447:22: warning: unused variable ‘loc’ [-Wunused-variable]
  447 |                 auto loc = o.Location(max_overhang_);
      |                      ^~~
g++ -o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/overlap_stat.cpp
ar rv ../Linux-amd64/bin/libfsa.a ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o
ar: creating ../Linux-amd64/bin/libfsa.a
a - ../Linux-amd64/obj/libfsa.a/app/fsa/argument_parser.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/getopt.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/logger.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/read_store.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/sequence.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/utility.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/fasta_reader.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/fastq_reader.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_store.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/simple_align.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_filter.o
a - ../Linux-amd64/obj/libfsa.a/app/fsa/overlap_stat.o
g++ -o ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_ol_filter.cpp
g++ -o ../Linux-amd64/bin/fsa_ol_filter -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_ol_filter/app/fsa/fsa_ol_filter.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp
g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_assemble.cpp
g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/assembly.cpp
g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/graph.cpp
g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/string_graph.cpp
app/fsa/string_graph.cpp: In member function ‘std::vector<StringNode*> StringNode::GetAllOutNodes()’:
app/fsa/string_graph.cpp:39:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
   39 |     return std::move(nodes);
      |            ~~~~~~~~~^~~~~~~
app/fsa/string_graph.cpp:39:21: note: remove ‘std::move’ call
app/fsa/string_graph.cpp: In member function ‘std::vector<StringNode*> StringNode::GetAllInNodes()’:
app/fsa/string_graph.cpp:49:21: warning: moving a local object in a return statement prevents copy elision [-Wpessimizing-move]
   49 |     return std::move(nodes);
      |            ~~~~~~~~~^~~~~~~
app/fsa/string_graph.cpp:49:21: note: remove ‘std::move’ call
g++ -o ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/path_graph.cpp
g++ -o ../Linux-amd64/bin/fsa_assemble -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_assemble/app/fsa/fsa_assemble.o ../Linux-amd64/obj/fsa_assemble/app/fsa/assembly.o ../Linux-amd64/obj/fsa_assemble/app/fsa/graph.o ../Linux-amd64/obj/fsa_assemble/app/fsa/string_graph.o ../Linux-amd64/obj/fsa_assemble/app/fsa/path_graph.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp
g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_ctg_bridge.cpp
g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_bridge.cpp
g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_graph.cpp
g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_link.cpp
g++ -o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/contig_link_store.cpp
g++ -o ../Linux-amd64/bin/fsa_ctg_bridge -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/fsa_ctg_bridge.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_bridge.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_graph.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link.o ../Linux-amd64/obj/fsa_ctg_bridge/app/fsa/contig_link_store.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp
g++ -o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/fsa_rd_stat.cpp
g++ -o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.o -c -MD -D_GLIBCXX_PARALLEL -pthread -O3 -Wall -std=c++11 -DNDEBUG -fopenmp -U_GLIBCXX_PARALLEL -std=c++11 -Wall -O3 -D_FILE_OFFSET_BITS=64 -Iapp/fsa app/fsa/read_stat.cpp
g++ -o ../Linux-amd64/bin/fsa_rd_stat -pthread -lm -lz -lstdc++ -fopenmp -L../Linux-amd64/bin ../Linux-amd64/obj/fsa_rd_stat/app/fsa/fsa_rd_stat.o ../Linux-amd64/obj/fsa_rd_stat/app/fsa/read_stat.o -lfsa -pthread -lm -lz -lstdc++ -fopenmp
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test
   create-stamp debian/debhelper-build-stamp
   dh_prep
   dh_auto_install --destdir=debian/mecat2/
   debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
sed 's/\#\!\/usr\/bin\/env perl/\#\!\/usr\/bin\/perl/' \
	debian/mecat2/usr/bin/mecat.pl > debian/mecat2/usr/bin/mecat
rm -f debian/mecat2/usr/bin/mecat.pl
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installdocs
   dh_installchangelogs
   dh_installman
   dh_lintian
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
dwz: debian/mecat2/usr/bin/fsa_assemble: .debug_info section not present
dwz: debian/mecat2/usr/bin/fsa_ctg_bridge: .debug_info section not present
dwz: debian/mecat2/usr/bin/fsa_ol_filter: .debug_info section not present
dwz: debian/mecat2/usr/bin/fsa_rd_stat: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2cns: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2extseqs: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2lcr: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2map: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2pcan: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2pm4: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2splitreads: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2trimbases: .debug_info section not present
dwz: debian/mecat2/usr/bin/mecat2viewdb: .debug_info section not present
dwz: Too few files for multifile optimization
dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it.
dh_dwz: warning: Common issues include no debug information at all (missing -g) and
dh_dwz: warning: compressed debug information (#931891).
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package 'mecat2' in '../mecat2_0.0+git20200428.f54c542+ds-4_amd64.deb'.
dpkg-deb: building package 'mecat2-dbgsym' in '../mecat2-dbgsym_0.0+git20200428.f54c542+ds-4_amd64.deb'.
 dpkg-genbuildinfo -O../mecat2_0.0+git20200428.f54c542+ds-4_amd64.buildinfo
 dpkg-genchanges -O../mecat2_0.0+git20200428.f54c542+ds-4_amd64.changes
dpkg-genchanges: info: not including original source code in upload
 dpkg-source -Zxz --after-build .
dpkg-buildpackage: info: binary and diff upload (original source NOT included)
--------------------------------------------------------------------------------
Build finished at 2024-06-04T15:35:24Z

Finished
--------

I: Built successfully

+------------------------------------------------------------------------------+
| Changes                                                                      |
+------------------------------------------------------------------------------+


mecat2_0.0+git20200428.f54c542+ds-4_amd64.changes:
--------------------------------------------------

Format: 1.8
Date: Tue, 07 Nov 2023 08:44:12 +0100
Source: mecat2
Binary: mecat2 mecat2-dbgsym
Architecture: source amd64
Version: 0.0+git20200428.f54c542+ds-4
Distribution: perl-5.40-throwaway
Urgency: medium
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 mecat2     - ultra-fast and accurate de novo assembly tools for SMRT reads
Closes: 1054708
Changes:
 mecat2 (0.0+git20200428.f54c542+ds-4) unstable; urgency=medium
 .
   * Team upload.
   * Add patch to fix FTBFS with gcc-13
     Closes: #1054708
   * Standards-Version: 4.6.2 (routine-update)
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+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

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Build-Date: Tue, 04 Jun 2024 15:35:21 +0000
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Environment:
 DEB_BUILD_OPTIONS="parallel=2"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 LC_COLLATE="C.UTF-8"
 LD_LIBRARY_PATH="/usr/lib/libeatmydata"
 SOURCE_DATE_EPOCH="1699343052"


+------------------------------------------------------------------------------+
| Package contents                                                             |
+------------------------------------------------------------------------------+


mecat2-dbgsym_0.0+git20200428.f54c542+ds-4_amd64.deb
----------------------------------------------------

 new Debian package, version 2.0.
 size 107712 bytes: control archive=1160 bytes.
     901 bytes,    12 lines      control
    1378 bytes,    13 lines      md5sums
 Package: mecat2-dbgsym
 Source: mecat2
 Version: 0.0+git20200428.f54c542+ds-4
 Auto-Built-Package: debug-symbols
 Architecture: amd64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1007
 Depends: mecat2 (= 0.0+git20200428.f54c542+ds-4)
 Section: debug
 Priority: optional
 Description: debug symbols for mecat2
 Build-Ids: 2222f66aaaf4e00b9fcf05c695cef955c0fdcc71 40cf578f53b41ec2faa1d4d801dbdeba0d30f0f1 428cea41200f2077dec0757d8e5375be4f20de98 72571f170ca4811de2f3108d1484b7f9060588d3 7d8e5efa26e918ad546fb4e17fd674b7ef883cd0 81e95cca7fa1e418a52edccb181dc7c4ef3a70c6 93636f7d10e42d0795fa341d189c906b4b6d5597 a0883334f79924f64de33d6b3fd17aa6e638376e a69102a20576e4cfd91fb2393674b2ffa45dc385 ac518feba749ac3dd4603fbbebdfc2aae059a642 d3f01571535163245e16948dab228426af74cb3a d58b8a69480bb2ecfdc9b47c0245863cd9bfa60b fd2854983692e3cf72ddf549e17042d1fda3770b

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lrwxrwxrwx root/root         0 2023-11-07 07:44 ./usr/share/doc/mecat2-dbgsym -> mecat2


mecat2_0.0+git20200428.f54c542+ds-4_amd64.deb
---------------------------------------------

 new Debian package, version 2.0.
 size 764004 bytes: control archive=1628 bytes.
     850 bytes,    16 lines      control
    1911 bytes,    31 lines      md5sums
 Package: mecat2
 Version: 0.0+git20200428.f54c542+ds-4
 Architecture: amd64
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 4052
 Depends: libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 13.1), zlib1g (>= 1:1.1.4), perl:any
 Section: science
 Priority: optional
 Homepage: https://github.com/xiaochuanle/MECAT2
 Description: ultra-fast and accurate de novo assembly tools for SMRT reads
  An improved version of MECAT. It is an ultra-fast and accurate mapping
  and error correcting de novo assembly tools for single molecula
  sequencing (SMRT) reads. MECAT2 consists of the following three modules:
   1. mecat2map: a fast and accurate alignment tool for SMRT reads.
   2. mecat2cns: correct noisy reads based on their pairwise overlaps.
   3. fsa: a string graph based assembly tool.

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drwxr-xr-x root/root         0 2023-11-07 07:44 ./usr/share/
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-rw-r--r-- root/root       443 2023-11-07 07:44 ./usr/share/doc/mecat2/changelog.Debian.gz
-rw-r--r-- root/root      6098 2023-11-07 07:44 ./usr/share/doc/mecat2/copyright
drwxr-xr-x root/root         0 2023-11-07 07:44 ./usr/share/lintian/
drwxr-xr-x root/root         0 2023-11-07 07:44 ./usr/share/lintian/overrides/
-rw-r--r-- root/root       804 2023-11-07 07:44 ./usr/share/lintian/overrides/mecat2
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drwxr-xr-x root/root         0 2023-11-07 07:44 ./usr/share/perl5/
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-rw-r--r-- root/root        80 2020-04-28 11:55 ./usr/share/perl5/Plgd/Grid.pm
-rw-r--r-- root/root      2747 2020-04-28 11:55 ./usr/share/perl5/Plgd/GridLsf.pm
-rw-r--r-- root/root      2122 2020-04-28 11:55 ./usr/share/perl5/Plgd/GridPbs.pm
-rw-r--r-- root/root      2069 2020-04-28 11:55 ./usr/share/perl5/Plgd/GridSge.pm
-rw-r--r-- root/root      3606 2020-04-28 11:55 ./usr/share/perl5/Plgd/GridSlurm.pm
-rw-r--r-- root/root      8768 2020-04-28 11:55 ./usr/share/perl5/Plgd/Project.pm
-rw-r--r-- root/root      4168 2020-04-28 11:55 ./usr/share/perl5/Plgd/Script.pm
-rw-r--r-- root/root      4390 2020-04-28 11:55 ./usr/share/perl5/Plgd/Utils.pm


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


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use

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

Build Architecture: amd64
Build Type: full
Build-Space: 685060
Build-Time: 157
Distribution: perl-5.40-throwaway
Host Architecture: amd64
Install-Time: 4
Job: /srv/debomatic/incoming/mecat2_0.0+git20200428.f54c542+ds-4.dsc
Machine Architecture: amd64
Package: mecat2
Package-Time: 176
Source-Version: 0.0+git20200428.f54c542+ds-4
Space: 685060
Status: successful
Version: 0.0+git20200428.f54c542+ds-4
--------------------------------------------------------------------------------
Finished at 2024-06-04T15:35:24Z
Build needed 00:02:56, 685060k disk space