Raspbian Package Auto-Building

Build log for centrifuge (1.0.3-10) on armhf

centrifuge → 1.0.3-10 → armhf → 2021-12-11 05:17:37 

sbuild (Debian sbuild) 0.78.1 (09 February 2019) on test2019

+==============================================================================+
| centrifuge 1.0.3-10 (armhf)                  Sat, 11 Dec 2021 05:08:32 +0000 |
+==============================================================================+

Package: centrifuge
Version: 1.0.3-10
Source Version: 1.0.3-10
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bookworm-staging-armhf-sbuild-56c0011d-4eb2-4620-aed0-dddb7549d380' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/centrifuge-VnaGkI/resolver-ldCWmc' with '<<RESOLVERDIR>>'

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

Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.6 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.5 MB]
Fetched 26.1 MB in 14s (1930 kB/s)
Reading package lists...

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: 'centrifuge' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/centrifuge.git
Please use:
git clone https://salsa.debian.org/med-team/centrifuge.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 718 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main centrifuge 1.0.3-10 (dsc) [2037 B]
Get:2 http://172.17.4.1/private bookworm-staging/main centrifuge 1.0.3-10 (tar) [701 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main centrifuge 1.0.3-10 (diff) [14.7 kB]
Fetched 718 kB in 1s (1249 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/centrifuge-VnaGkI/centrifuge-1.0.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/centrifuge-VnaGkI' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-python3, jellyfish, build-essential, fakeroot
Filtered Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-python3, jellyfish, build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [396 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [479 B]
Fetched 1832 B in 0s (47.8 kB/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
  gettext-base groff-base intltool-debian jellyfish libarchive-zip-perl
  libbrotli1 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1
  libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu67
  libjellyfish-2.0-2 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14
  libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal
  libpython3.9-stdlib librtmp1 libsigsegv2 libssh2-1 libsub-override-perl
  libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3
  python3-distutils python3-lib2to3 python3-minimal python3.9
  python3.9-minimal
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make flit python3-toml
  gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran
  | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
  libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv
  python3.9-doc binfmt-support
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl publicsuffix
  libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
  gettext-base groff-base intltool-debian jellyfish libarchive-zip-perl
  libbrotli1 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1
  libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu67
  libjellyfish-2.0-2 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14
  libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal
  libpython3.9-stdlib librtmp1 libsigsegv2 libssh2-1 libsub-override-perl
  libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3
  python3-distutils python3-lib2to3 python3-minimal python3.9
  python3.9-minimal sbuild-build-depends-main-dummy
0 upgraded, 55 newly installed, 0 to remove and 17 not upgraded.
Need to get 24.6 MB of archives.
After this operation, 91.0 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://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.2-4 [135 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-7 [793 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.4-1 [31.6 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.9-1+rpi1 [795 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.1-3 [80.1 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.9-1+rpi1 [1582 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.7-1 [38.4 kB]
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Get:12 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.9-1+rpi1 [1609 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf python3.9 armhf 3.9.9-1+rpi1 [484 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.7-1 [21.6 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.9.7-1 [38.0 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.5.2 [192 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.12.1-1 [26.5 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.12.1-1 [15.6 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.5.2 [1056 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.9-2 [79.5 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.9.9-2 [146 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20211114 [104 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.79.1-2 [317 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libjellyfish-2.0-2 armhf 2.3.0-12 [56.4 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf jellyfish armhf 2.3.0-12 [621 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up media-types (4.0.0) ...
Setting up libpipeline1:armhf (1.5.4-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up bsdextrautils (2.37.2-4) ...
update-alternatives: using /usr/bin/write.ul to provide /usr/bin/write (write) in auto mode
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.41-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.5.2) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.41-2) ...
Setting up libdeflate0:armhf (1.8-1) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.41-2) ...
Setting up libjellyfish-2.0-2:armhf (2.3.0-12) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up autopoint (0.21-4) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up libelf1:armhf (0.186-1) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libpython3.9-stdlib:armhf (3.9.9-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.7-1) ...
Setting up libfile-stripnondeterminism-perl (1.12.1-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.79.1-2) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.12.1-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-7) ...
Setting up python3.9 (3.9.9-1+rpi1) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.13+ds-2) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.9.7-1) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up jellyfish (2.3.0-12) ...
Setting up python3-lib2to3 (3.9.9-2) ...
Setting up python3-distutils (3.9.9-2) ...
Setting up dh-python (5.20211114) ...
Setting up debhelper (13.5.2) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.32-4+rpi1) ...

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

Arch check ok (armhf included in any)

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

Kernel: Linux 4.19.20-v7+ #1 SMP Mon Mar 18 11:37:02 GMT 2019 armhf (armv7l)
Toolchain package versions: binutils_2.37-7+rpi1 dpkg-dev_1.20.9+rpi1 g++-11_11.2.0-10+rpi1 gcc-11_11.2.0-10+rpi1 libc6-dev_2.32-4+rpi1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.13 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-5 binutils_2.37-7+rpi1 binutils-arm-linux-gnueabihf_2.37-7+rpi1 binutils-common_2.37-7+rpi1 bsdextrautils_2.37.2-4 bsdutils_1:2.37.2-4 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-10+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.5.2 debianutils_4.11.2 dh-autoreconf_20 dh-python_5.20211114 dh-strip-nondeterminism_1.12.1-1 diffutils_1:3.7-5 dirmngr_2.2.27-2 dpkg_1.20.9+rpi1 dpkg-dev_1.20.9+rpi1 dwz_0.14-1 e2fsprogs_1.46.4-1 fakeroot_1.25.3-1.1 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-10+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-10+rpi1 gcc-11-base_11.2.0-10+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-2 gnupg-l10n_2.2.27-2 gnupg-utils_2.2.27-2 gpg_2.2.27-2 gpg-agent_2.2.27-2 gpg-wks-client_2.2.27-2 gpg-wks-server_2.2.27-2 gpgconf_2.2.27-2 gpgsm_2.2.27-2 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 jellyfish_2.3.0-12 libacl1_2.3.1-1 libapt-pkg6.0_2.3.13 libarchive-zip-perl_1.68-1 libasan6_11.2.0-10+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-10+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37-7+rpi1 libblkid1_2.37.2-4 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-4 libc-bin_2.32-4+rpi1 libc-dev-bin_2.32-4+rpi1 libc6_2.32-4+rpi1 libc6-dev_2.32-4+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-10+rpi1 libcom-err2_1.46.4-1 libcrypt-dev_1:4.4.26-1 libcrypt1_1:4.4.26-1 libctf-nobfd0_2.37-7+rpi1 libctf0_2.37-7+rpi1 libcurl3-gnutls_7.79.1-2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.5.2 libdeflate0_1.8-1 libdpkg-perl_1.20.9+rpi1 libelf1_0.186-1 libexpat1_2.4.1-3 libext2fs2_1.46.4-1 libfakeroot_1.25.3-1.1 libffi8_3.4.2-3 libfile-stripnondeterminism-perl_1.12.1-1 libgcc-11-dev_11.2.0-10+rpi1 libgcc-s1_11.2.0-10+rpi1 libgcrypt20_1.9.4-3 libgdbm-compat4_1.22-1 libgdbm6_1.22-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.2-2 libgomp1_11.2.0-10+rpi1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjellyfish-2.0-2_2.3.0-12 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmount1_2.37.2-4 libmpc3_1.2.1-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.3-1 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-5 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.4-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.7-1 libpython3.9-minimal_3.9.9-1+rpi1 libpython3.9-stdlib_3.9.9-1+rpi1 libreadline8_8.1-2 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg2-2 libsasl2-modules-db_2.1.27+dfsg2-2 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.13-1 libsmartcols1_2.37.2-4 libsqlite3-0_3.36.0-2 libss2_1.46.4-1 libssh2-1_1.10.0-2 libssl1.1_1.1.1l-1 libstdc++-11-dev_11.2.0-10+rpi1 libstdc++6_11.2.0-10+rpi1 libsub-override-perl_0.09-2 libsystemd0_249.7-1+rpi1 libtasn1-6_4.18.0-4 libtext-charwidth-perl_0.04-10+b1 libtext-iconv-perl_1.7-7+b1 libtinfo6_6.3-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-10+rpi1 libuchardet0_0.0.7-1 libudev1_249.7-1+rpi1 libunistring2_0.9.10-6 libuuid1_2.37.2-4 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.8.1-2 logsave_1.46.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-4 ncurses-base_6.3-1 ncurses-bin_6.3-1 passwd_1:4.8.1-2 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.7-1 python3-distutils_3.9.9-2 python3-lib2to3_3.9.9-2 python3-minimal_3.9.7-1 python3.9_3.9.9-1+rpi1 python3.9-minimal_3.9.9-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.2-4 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2

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


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

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

Format: 3.0 (quilt)
Source: centrifuge
Binary: centrifuge
Architecture: any
Version: 1.0.3-10
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Andreas Tille <tille@debian.org>
Homepage: https://ccb.jhu.edu/software/centrifuge/
Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/centrifuge
Vcs-Git: https://salsa.debian.org/med-team/centrifuge.git
Testsuite: autopkgtest
Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-python3, jellyfish
Package-List:
 centrifuge deb science optional arch=any
Checksums-Sha1:
 c31fc38298b74f5b81f1d3704f7c4311231d6bc0 701273 centrifuge_1.0.3.orig.tar.gz
 0eb841acad6784aa526f8bf29ac8102b5f98f501 14660 centrifuge_1.0.3-10.debian.tar.xz
Checksums-Sha256:
 71340f5c0c20dd4f7c4d98ea87f9edcbb1443fff8434e816a5465cbebaca9343 701273 centrifuge_1.0.3.orig.tar.gz
 6bc0d1ac340554bb4db925a246ba48a942d50256dafb27353e5b41d2a2359111 14660 centrifuge_1.0.3-10.debian.tar.xz
Files:
 4ab20730ae43f26a98b754d83213e10c 701273 centrifuge_1.0.3.orig.tar.gz
 083a6b1cfc1eaa3a475e376c5f39140a 14660 centrifuge_1.0.3-10.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.9DTotFrT/trustedkeys.kbx': General error
gpgv: Signature made Sun Dec  5 20:20:35 2021 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./centrifuge_1.0.3-10.dsc
dpkg-source: info: extracting centrifuge in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking centrifuge_1.0.3.orig.tar.gz
dpkg-source: info: unpacking centrifuge_1.0.3-10.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_auto_ptr_usage_in_gcc-7.patch
dpkg-source: info: applying 0002-Fix-build-with-rank.patch
dpkg-source: info: applying 0003-Fix-make-install-DESTDIR.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying no_msse2.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying fix_arm_build.patch

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=1b2d35e96e094e0c905e1f5e00ab4580
JOURNAL_STREAM=8:29072680
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-56c0011d-4eb2-4620-aed0-dddb7549d380
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c190696
XDG_SESSION_TYPE=unspecified

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

Command: dpkg-buildpackage -us -uc -mRaspbian pi4 based autobuilder <root@raspbian.org> -B -rfakeroot
dpkg-buildpackage: info: source package centrifuge
dpkg-buildpackage: info: source version 1.0.3-10
dpkg-buildpackage: info: source distribution unstable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
 debian/rules clean
dh clean --with python3
   dh_auto_clean
	make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f centrifuge-build-bin centrifuge-class centrifuge-inspect-bin centrifuge-build-bin-debug centrifuge-class-debug centrifuge-inspect-bin-debug \
centrifuge-build-bin.exe centrifuge-class.exe centrifuge-inspect-bin.exe centrifuge-build-bin-debug.exe centrifuge-class-debug.exe centrifuge-inspect-bin-debug.exe \
centrifuge-src.zip centrifuge-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
 debian/rules binary-arch
dh binary-arch --with python3
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- BITS=32 BITS_FLAG=
	make -j4 "INSTALL=install --strip-program=true" BITS=32 BITS_FLAG=
make[2]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/g++  -O3   -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 \""  \
-fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security  -DBOWTIE_MM  -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
 \
-o centrifuge-build-bin centrifuge_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp centrifuge_build_main.cpp \
-lpthread 
/usr/bin/g++  -O3   -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 \""  \
-fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security  -DBOWTIE_MM  -Wl,-z,relro -Wl,-z,now  -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
  \
-o centrifuge-class centrifuge.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp ref_coord.cpp mask.cpp pe.cpp aligner_seed_policy.cpp scoring.cpp presets.cpp simple_func.cpp random_util.cpp outq.cpp centrifuge_main.cpp \
-lpthread  
/usr/bin/g++  -O3   -funroll-loops -g3 \
-DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 \""  \
-fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++  -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security  -DBOWTIE_MM  -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
 -I . \
-o centrifuge-inspect-bin centrifuge_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread 
In file included from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                         ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                                                   ^~~~~
diff_sample.h:176:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                         ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                                                   ^~~~~
In file included from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  490 |                 mkeyQSortSuf(t, s, slen, 4,
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  491 |                              this->verbose(), this->sanityCheck());
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge.cpp:34:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                         ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                                                   ^~~~~
diff_sample.h:176:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                         ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                                                   ^~~~~
In file included from bt2_idx.h:44,
                 from centrifuge.cpp:34:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  490 |                 mkeyQSortSuf(t, s, slen, 4,
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  491 |                              this->verbose(), this->sanityCheck());
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                                      ^~~~~~~~
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:15:   required from here
multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |         if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro ‘OFF_MASK’
 1155 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro ‘OFF_MASK’
 1164 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
In file included from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from hier_idx.h:24,
                 from centrifuge_inspect.cpp:28:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                         ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                                                   ^~~~~
diff_sample.h:176:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                         ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                                                   ^~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro ‘OFF_MASK’
 1066 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1062:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’
  914 |                         off = OFF_MASK;
      |                               ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’
  923 |                                                                OFF_MASK, begin, end);
      |                                                                ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’
 1007 |                 sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                              ^~~~~~~~
In file included from bt2_idx.h:44,
                 from hier_idx.h:24,
                 from centrifuge_inspect.cpp:28:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  490 |                 mkeyQSortSuf(t, s, slen, 4,
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  491 |                              this->verbose(), this->sanityCheck());
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from centrifuge_build.cpp:27:
bt2_idx.h: In instantiation of ‘void Ebwt<index_t>::buildToDisk(InorderBlockwiseSA<TStr>&, const TStr&, std::ostream&, std::ostream&, std::ostream*, std::ostream*, const EList<RefRecord>&, int) [with TStr = SString<char>; index_t = long long unsigned int; std::ostream = std::basic_ostream<char>]’:
bt2_idx.h:1492:16:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
bt2_idx.h:3452:41: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
 3452 |                     for(size_t k = 0; k < kmer_size; k++) {
      |                                       ~~^~~~~~~~~~~
bt2_idx.h:3641:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
 3641 |       for(size_t k = 0; k < kmer_size; k++) {
      |                         ~~^~~~~~~~~~~
bt2_idx.h: In instantiation of ‘void Ebwt<index_t>::buildToDisk(InorderBlockwiseSA<TStr>&, const TStr&, std::ostream&, std::ostream&, std::ostream*, std::ostream*, const EList<RefRecord>&, int) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ostream = std::basic_ostream<char>]’:
bt2_idx.h:1492:16:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:697:25:   required from here
bt2_idx.h:3452:41: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
 3452 |                     for(size_t k = 0; k < kmer_size; k++) {
      |                                       ~~^~~~~~~~~~~
bt2_idx.h:3641:27: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
 3641 |       for(size_t k = 0; k < kmer_size; k++) {
      |                         ~~^~~~~~~~~~~
In file included from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
diff_sample.h: In instantiation of ‘void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]’:
blockwise_sa.h:383:20:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  813 |                     sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v);
      |                     ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
diff_sample.h: In instantiation of ‘void DifferenceCoverSample<T>::build(int) [with TStr = S2bDnaString]’:
blockwise_sa.h:383:20:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:697:25:   required from here
diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList<unsigned int>*) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
diff_sample.h:772:30:   required from ‘void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]’
blockwise_sa.h:383:20:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
multikey_qsort.h:661:39: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  661 |                 sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                 ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’:
blockwise_sa.h:607:9:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:388:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
blockwise_sa.h:460:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  460 |                 mkeyQSortSuf(t, s, slen, 4,
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  461 |                              this->verbose(), this->sanityCheck());
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h:460:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList<unsigned int>*) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
diff_sample.h:772:30:   required from ‘void DifferenceCoverSample<T>::build(int) [with TStr = S2bDnaString]’
blockwise_sa.h:383:20:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:697:25:   required from here
multikey_qsort.h:661:39: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  661 |                 sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                 ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:454:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:607:9:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:388:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                                      ^~~~~~~~
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:460:15:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:607:9:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:388:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |         if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:454:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:607:9:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:388:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro ‘OFF_MASK’
 1155 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro ‘OFF_MASK’
 1164 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:454:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:607:9:   required from ‘void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]’
blockwise_sa.h:388:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro ‘OFF_MASK’
 1066 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1062:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:454:19:   required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:607:9:   [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
blockwise_sa.h:362:4:   required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:215:29:   required from ‘KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]’
bt2_idx.h:1488:33:   required from ‘void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
bt2_idx.h:881:23:   required from ‘Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
centrifuge_build.cpp:472:19:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
centrifuge_build.cpp:677:28:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’
  914 |                         off = OFF_MASK;
      |                               ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’
  923 |                                                                OFF_MASK, begin, end);
      |                                                                ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’
 1007 |                 sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                              ^~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge.cpp:34:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                                      ^~~~~~~~
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge.cpp:34:
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:15:   required from here
multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |         if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from centrifuge.cpp:47:
classifier.h: In instantiation of ‘int Classifier<index_t, local_index_t>::go(const Scoring&, const Ebwt<index_t>&, const Ebwt<index_t>&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, SpeciesMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’:
centrifuge.cpp:2660:34:   required from here
classifier.h:411:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
  411 |                     if(i + 1 < _hitMap.size()) {
      |                        ~~~~~~^~~~~~~~~~~~~~~~
classifier.h:432:48: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
  432 |                         if(_hitMap[i].rank + 1 >= _hitMap[i].path.size()) {
      |                            ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
classifier.h:442:55: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
  442 |                     uint64_t parent_taxID = (rank + 1 >= _hitMap[i].path.size() ? 1 : _hitMap[i].path[rank + 1]);
      |                                              ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
classifier.h:475:63: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
  475 |                         uint64_t cur_parent_taxID = (rank + 1 >= _hitMap[i].path.size() ? 1 : _hitMap[i].path[rank + 1]);
      |                                                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge.cpp:34:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro ‘OFF_MASK’
 1155 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro ‘OFF_MASK’
 1164 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
In file included from centrifuge.cpp:47:
classifier.h: In instantiation of ‘void Classifier<index_t, local_index_t>::searchForwardAndReverse(index_t, const Ebwt<index_t>&, const Scoring&, RandomSource&, const ReportingParams&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’:
classifier.h:238:13:   required from ‘int Classifier<index_t, local_index_t>::go(const Scoring&, const Ebwt<index_t>&, const Ebwt<index_t>&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, SpeciesMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
centrifuge.cpp:2660:34:   required from here
classifier.h:850:50: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
  850 |                        hit.size() + rchit.size() > rp.ihits) {
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
classifier.h:647:16: warning: variable ‘cur’ set but not used [-Wunused-but-set-variable]
  647 |         size_t cur[2] = {0, 0} ;
      |                ^~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from centrifuge.cpp:34:
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro ‘OFF_MASK’
 1066 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1062:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’
  914 |                         off = OFF_MASK;
      |                               ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’
  923 |                                                                OFF_MASK, begin, end);
      |                                                                ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’
 1007 |                 sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                              ^~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from hier_idx.h:24,
                 from centrifuge_inspect.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                                      ^~~~~~~~
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from hier_idx.h:24,
                 from centrifuge_inspect.cpp:28:
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:15:   required from here
multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |         if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from centrifuge.cpp:41:
aln_sink.h: In instantiation of ‘void AlnSinkSam<index_t>::appendMate(Ebwt<index_t>&, BTString&, const Read&, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable<char, 1024, 2>; TReadId = long long unsigned int; size_t = unsigned int]’:
aln_sink.h:1407:9:   required from ‘void AlnSinkSam<index_t>::append(BTString&, size_t, const Read*, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, bool, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable<char, 1024, 2>; size_t = unsigned int; TReadId = long long unsigned int]’
aln_sink.h:1392:15:   required from here
aln_sink.h:2302:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
 2302 |         for (int i=0; i < this->tab_fmt_cols_.size(); ++i) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from hier_idx.h:24,
                 from centrifuge_inspect.cpp:28:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro ‘OFF_MASK’
 1155 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro ‘OFF_MASK’
 1164 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro ‘OFF_MASK’
 1066 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1062:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’
  914 |                         off = OFF_MASK;
      |                               ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’
  923 |                                                                OFF_MASK, begin, end);
      |                                                                ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’
 1007 |                 sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                              ^~~~~~~~
In file included from /usr/include/c++/11/set:60,
                 from centrifuge_inspect.cpp:24:
/usr/include/c++/11/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const long long unsigned int&>, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, long long unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, long long unsigned int> >]’:
/usr/include/c++/11/bits/stl_tree.h:2426:7: note: parameter passing for argument of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned int> > >::const_iterator’ changed in GCC 7.1
 2426 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
                 from bt2_idx.h:34,
                 from hier_idx.h:24,
                 from centrifuge_inspect.cpp:28:
/usr/include/c++/11/bits/stl_map.h: In constructor ‘Ebwt<index_t>::Ebwt(const string&, int, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = long long unsigned int]’:
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned int> > >::const_iterator’ changed in GCC 7.1
  501 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type ‘std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned int> > >::const_iterator’ changed in GCC 7.1
  501 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  502 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  503 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In file included from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                         ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                                                   ^~~~~
diff_sample.h:176:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                         ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                                                   ^~~~~
In file included from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  490 |                 mkeyQSortSuf(t, s, slen, 4,
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  491 |                              this->verbose(), this->sanityCheck());
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                                      ^~~~~~~~
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:15:   required from here
multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |         if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro ‘OFF_MASK’
 1155 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro ‘OFF_MASK’
 1164 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro ‘OFF_MASK’
 1066 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1062:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’
  914 |                         off = OFF_MASK;
      |                               ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’
  923 |                                                                OFF_MASK, begin, end);
      |                                                                ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’
 1007 |                 sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                              ^~~~~~~~
In file included from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                         ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                                                   ^~~~~
diff_sample.h:176:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                         ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                                                   ^~~~~
In file included from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  490 |                 mkeyQSortSuf(t, s, slen, 4,
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  491 |                              this->verbose(), this->sanityCheck());
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                                      ^~~~~~~~
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:15:   required from here
multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |         if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro ‘OFF_MASK’
 1155 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro ‘OFF_MASK’
 1164 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro ‘OFF_MASK’
 1066 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1062:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’
  914 |                         off = OFF_MASK;
      |                               ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’
  923 |                                                                OFF_MASK, begin, end);
      |                                                                ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’
 1007 |                 sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                              ^~~~~~~~
In file included from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                         ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                                                   ^~~~~
diff_sample.h:176:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                         ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                                                   ^~~~~
In file included from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  490 |                 mkeyQSortSuf(t, s, slen, 4,
      |                 ~~~~~~~~~~~~^~~~~~~~~~~~~~~
  491 |                              this->verbose(), this->sanityCheck());
      |                              ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]’:
blockwise_sa.h:490:29: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro ‘OFF_MASK’
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                                                                      ^~~~~~~~
In file included from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  764 |         if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:490:15:   required from here
multikey_qsort.h:496:47: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
  496 |         if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
                 from sequence_io.h:28,
                 from multikey_qsort.h:24,
                 from diff_sample.h:26,
                 from blockwise_sa.h:29,
                 from bt2_idx.h:44,
                 from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro ‘OFF_MASK’
 1155 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro ‘OFF_MASK’
 1164 |                         sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                                      ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro ‘OFF_MASK’
 1066 |                                        OFF_MASK, begin, end);
      |                                        ^~~~~~~~
multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’:
multikey_qsort.h:1062:33:   required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’
multikey_qsort.h:1161:20:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
multikey_qsort.h:763:18:   required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’
blockwise_sa.h:484:19:   required from here
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro ‘OFF_MASK’
  914 |                         off = OFF_MASK;
      |                               ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro ‘OFF_MASK’
  923 |                                                                OFF_MASK, begin, end);
      |                                                                ^~~~~~~~
btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
   25 | #define OFF_MASK 0xffffffffffffffff
      |                  ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro ‘OFF_MASK’
 1007 |                 sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
      |                                                              ^~~~~~~~
In file included from diff_sample.cpp:20:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:175:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                         ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  175 |                                         if(!diffs[d1]) diffCnt++; diffs[d1] = true;
      |                                                                   ^~~~~
diff_sample.h:176:41: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                         ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
  176 |                                         if(!diffs[d2]) diffCnt++; diffs[d2] = true;
      |                                                                   ^~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_auto_test -a
   create-stamp debian/debhelper-build-stamp
   dh_prep -a
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- prefix=/usr/lib/centrifuge
	make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/centrifuge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" prefix=/usr/lib/centrifuge
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/bin
mkdir -p /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/indices
install -m 0644 indices/Makefile /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/indices
install -d -m 0755 /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc
install -m 0644 doc/* /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc
for file in centrifuge-build-bin centrifuge-class centrifuge-inspect-bin centrifuge centrifuge-build centrifuge-inspect centrifuge-download centrifuge-kreport centrifuge-BuildSharedSequence.pl centrifuge-RemoveEmptySequence.pl centrifuge-RemoveN.pl centrifuge-compress.pl centrifuge-sort-nt.pl; do \
	install -m 0755 $file /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/bin ; \
done
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
mv debian/centrifuge/usr/lib/centrifuge/bin/* debian/centrifuge/usr/lib/centrifuge/
rmdir debian/centrifuge/usr/lib/centrifuge/bin
# move documentation to correct location
mkdir -p debian/centrifuge/usr/share/doc/centrifuge/html
mv debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc/*html \
   debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc/*css  \
   debian/centrifuge/usr/share/doc/centrifuge/html
# remove useless stuff in documentation dir
rm -rf debian/centrifuge/usr/lib/centrifuge/share/doc/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
    sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
rm -rf debian/*/usr/lib/centrifuge/share/centrifuge/doc
find debian -name manual.inc.html | xargs rm -rf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installdocs -a
   dh_installchangelogs -a
   dh_installman -a
   dh_python3 -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
   dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/centrifuge/usr/lib/centrifuge/centrifuge-class contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/centrifuge/usr/lib/centrifuge/centrifuge-build-bin contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/centrifuge/usr/lib/centrifuge/centrifuge-inspect-bin contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/centrifuge/usr/lib/centrifuge/centrifuge-class debian/centrifuge/usr/lib/centrifuge/centrifuge-build-bin debian/centrifuge/usr/lib/centrifuge/centrifuge-inspect-bin were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
   dh_installdeb -a
   dh_gencontrol -a
dpkg-gencontrol: warning: package centrifuge: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package centrifuge: substitution variable ${perl:Depends} unused, but is defined
   dh_md5sums -a
   dh_builddeb -a
dpkg-deb: building package 'centrifuge' in '../centrifuge_1.0.3-10_armhf.deb'.
dpkg-deb: building package 'centrifuge-dbgsym' in '../centrifuge-dbgsym_1.0.3-10_armhf.deb'.
 dpkg-genbuildinfo --build=any
 dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> >../centrifuge_1.0.3-10_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
 dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2021-12-11T05:17:31Z

Finished
--------

I: Built successfully

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


centrifuge_1.0.3-10_armhf.changes:
----------------------------------

Format: 1.8
Date: Sun, 05 Dec 2021 21:16:55 +0100
Source: centrifuge
Binary: centrifuge centrifuge-dbgsym
Architecture: armhf
Version: 1.0.3-10
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
 centrifuge - rapid and memory-efficient system for classification of DNA seque
Changes:
 centrifuge (1.0.3-10) unstable; urgency=medium
 .
   * Really fix watch file
Checksums-Sha1:
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 87890afc2f6a759a295d5458e5e51d7282661140 6018 centrifuge_1.0.3-10_armhf.buildinfo
 3d4a5c23704baeae0c92c5c66d9bcb681a376034 464268 centrifuge_1.0.3-10_armhf.deb
Checksums-Sha256:
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 47d9e2ca2975d1046a32b3bda981e4a222b2db170d3dbfe6f015203b12336b6a 6018 centrifuge_1.0.3-10_armhf.buildinfo
 ca96de1bb9363857ae09bd7db09b5b4878dfdae96fd8cc3a4d35052e83cba967 464268 centrifuge_1.0.3-10_armhf.deb
Files:
 4f712a00630c76f4229086faf0dcea3f 3402288 debug optional centrifuge-dbgsym_1.0.3-10_armhf.deb
 6f28f5dd45c2f1dbabcf6effc45faaa1 6018 science optional centrifuge_1.0.3-10_armhf.buildinfo
 99c2a2ece39c85399903b1a06f680fa7 464268 science optional centrifuge_1.0.3-10_armhf.deb

+------------------------------------------------------------------------------+
| Buildinfo                                                                    |
+------------------------------------------------------------------------------+

Format: 1.0
Source: centrifuge
Binary: centrifuge centrifuge-dbgsym
Architecture: armhf
Version: 1.0.3-10
Checksums-Md5:
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Checksums-Sha256:
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 ca96de1bb9363857ae09bd7db09b5b4878dfdae96fd8cc3a4d35052e83cba967 464268 centrifuge_1.0.3-10_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 11 Dec 2021 05:17:30 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
 autoconf (= 2.71-2),
 automake (= 1:1.16.5-1.1),
 autopoint (= 0.21-4),
 autotools-dev (= 20180224.1+nmu1),
 base-files (= 12+rpi1),
 base-passwd (= 3.5.52),
 bash (= 5.1-5),
 binutils (= 2.37-7+rpi1),
 binutils-arm-linux-gnueabihf (= 2.37-7+rpi1),
 binutils-common (= 2.37-7+rpi1),
 bsdextrautils (= 2.37.2-4),
 bsdutils (= 1:2.37.2-4),
 build-essential (= 12.9),
 bzip2 (= 1.0.8-4),
 coreutils (= 8.32-4.1),
 cpp (= 4:11.2.0-2+rpi1),
 cpp-11 (= 11.2.0-10+rpi1),
 dash (= 0.5.11+git20210903+057cd650a4ed-3),
 debconf (= 1.5.79),
 debhelper (= 13.5.2),
 debianutils (= 4.11.2),
 dh-autoreconf (= 20),
 dh-python (= 5.20211114),
 dh-strip-nondeterminism (= 1.12.1-1),
 diffutils (= 1:3.7-5),
 dpkg (= 1.20.9+rpi1),
 dpkg-dev (= 1.20.9+rpi1),
 dwz (= 0.14-1),
 file (= 1:5.41-2),
 findutils (= 4.8.0-1),
 g++ (= 4:11.2.0-2+rpi1),
 g++-11 (= 11.2.0-10+rpi1),
 gcc (= 4:11.2.0-2+rpi1),
 gcc-11 (= 11.2.0-10+rpi1),
 gcc-11-base (= 11.2.0-10+rpi1),
 gettext (= 0.21-4),
 gettext-base (= 0.21-4),
 grep (= 3.7-1),
 groff-base (= 1.22.4-7),
 gzip (= 1.10-4),
 hostname (= 3.23),
 init-system-helpers (= 1.60),
 intltool-debian (= 0.35.0+20060710.5),
 jellyfish (= 2.3.0-12),
 libacl1 (= 2.3.1-1),
 libarchive-zip-perl (= 1.68-1),
 libasan6 (= 11.2.0-10+rpi1),
 libatomic1 (= 11.2.0-10+rpi1),
 libattr1 (= 1:2.5.1-1),
 libaudit-common (= 1:3.0.6-1),
 libaudit1 (= 1:3.0.6-1),
 libbinutils (= 2.37-7+rpi1),
 libblkid1 (= 2.37.2-4),
 libbrotli1 (= 1.0.9-2+b1),
 libbz2-1.0 (= 1.0.8-4),
 libc-bin (= 2.32-4+rpi1),
 libc-dev-bin (= 2.32-4+rpi1),
 libc6 (= 2.32-4+rpi1),
 libc6-dev (= 2.32-4+rpi1),
 libcap-ng0 (= 0.7.9-2.2+b1),
 libcap2 (= 1:2.44-1),
 libcc1-0 (= 11.2.0-10+rpi1),
 libcom-err2 (= 1.46.4-1),
 libcrypt-dev (= 1:4.4.26-1),
 libcrypt1 (= 1:4.4.26-1),
 libctf-nobfd0 (= 2.37-7+rpi1),
 libctf0 (= 2.37-7+rpi1),
 libcurl3-gnutls (= 7.79.1-2),
 libdb5.3 (= 5.3.28+dfsg1-0.8),
 libdebconfclient0 (= 0.261),
 libdebhelper-perl (= 13.5.2),
 libdeflate0 (= 1.8-1),
 libdpkg-perl (= 1.20.9+rpi1),
 libelf1 (= 0.186-1),
 libexpat1 (= 2.4.1-3),
 libffi8 (= 3.4.2-3),
 libfile-stripnondeterminism-perl (= 1.12.1-1),
 libgcc-11-dev (= 11.2.0-10+rpi1),
 libgcc-s1 (= 11.2.0-10+rpi1),
 libgcrypt20 (= 1.9.4-3),
 libgdbm-compat4 (= 1.22-1),
 libgdbm6 (= 1.22-1),
 libgmp10 (= 2:6.2.1+dfsg-3),
 libgnutls30 (= 3.7.2-2),
 libgomp1 (= 11.2.0-10+rpi1),
 libgpg-error0 (= 1.42-3),
 libgssapi-krb5-2 (= 1.18.3-7),
 libhogweed6 (= 3.7.3-1),
 libhts3 (= 1.13+ds-2),
 libhtscodecs2 (= 1.1.1-3),
 libicu67 (= 67.1-7),
 libidn2-0 (= 2.3.2-2),
 libisl23 (= 0.24-2),
 libjellyfish-2.0-2 (= 2.3.0-12),
 libk5crypto3 (= 1.18.3-7),
 libkeyutils1 (= 1.6.1-2),
 libkrb5-3 (= 1.18.3-7),
 libkrb5support0 (= 1.18.3-7),
 libldap-2.4-2 (= 2.4.59+dfsg-1),
 liblz4-1 (= 1.9.3-2),
 liblzma5 (= 5.2.5-2),
 libmagic-mgc (= 1:5.41-2),
 libmagic1 (= 1:5.41-2),
 libmount1 (= 2.37.2-4),
 libmpc3 (= 1.2.1-1),
 libmpdec3 (= 2.5.1-2+rpi1),
 libmpfr6 (= 4.1.0-3),
 libncursesw6 (= 6.3-1),
 libnettle8 (= 3.7.3-1),
 libnghttp2-14 (= 1.43.0-1),
 libnsl-dev (= 1.3.0-2),
 libnsl2 (= 1.3.0-2),
 libp11-kit0 (= 0.24.0-5),
 libpam-modules (= 1.4.0-10),
 libpam-modules-bin (= 1.4.0-10),
 libpam-runtime (= 1.4.0-10),
 libpam0g (= 1.4.0-10),
 libpcre2-8-0 (= 10.39-3),
 libpcre3 (= 2:8.39-13),
 libperl5.32 (= 5.32.1-6),
 libpipeline1 (= 1.5.4-1),
 libpsl5 (= 0.21.0-1.2),
 libpython3-stdlib (= 3.9.7-1),
 libpython3.9-minimal (= 3.9.9-1+rpi1),
 libpython3.9-stdlib (= 3.9.9-1+rpi1),
 libreadline8 (= 8.1-2),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
 libsasl2-2 (= 2.1.27+dfsg2-2),
 libsasl2-modules-db (= 2.1.27+dfsg2-2),
 libseccomp2 (= 2.5.3-2+rpi1),
 libselinux1 (= 3.3-1),
 libsigsegv2 (= 2.13-1),
 libsmartcols1 (= 2.37.2-4),
 libsqlite3-0 (= 3.36.0-2),
 libssh2-1 (= 1.10.0-2),
 libssl1.1 (= 1.1.1l-1),
 libstdc++-11-dev (= 11.2.0-10+rpi1),
 libstdc++6 (= 11.2.0-10+rpi1),
 libsub-override-perl (= 0.09-2),
 libsystemd0 (= 249.7-1+rpi1),
 libtasn1-6 (= 4.18.0-4),
 libtinfo6 (= 6.3-1),
 libtirpc-common (= 1.3.2-2),
 libtirpc-dev (= 1.3.2-2),
 libtirpc3 (= 1.3.2-2),
 libtool (= 2.4.6-15),
 libubsan1 (= 11.2.0-10+rpi1),
 libuchardet0 (= 0.0.7-1),
 libudev1 (= 249.7-1+rpi1),
 libunistring2 (= 0.9.10-6),
 libuuid1 (= 2.37.2-4),
 libxml2 (= 2.9.12+dfsg-5),
 libzstd1 (= 1.4.8+dfsg-3+rpi1),
 linux-libc-dev (= 5.14.16-1+rpi1),
 login (= 1:4.8.1-2),
 lsb-base (= 11.1.0+rpi1),
 m4 (= 1.4.18-5),
 make (= 4.3-4.1),
 man-db (= 2.9.4-2),
 mawk (= 1.3.4.20200120-2),
 media-types (= 4.0.0),
 ncurses-base (= 6.3-1),
 ncurses-bin (= 6.3-1),
 patch (= 2.7.6-7),
 perl (= 5.32.1-6),
 perl-base (= 5.32.1-6),
 perl-modules-5.32 (= 5.32.1-6),
 po-debconf (= 1.0.21+nmu1),
 python3 (= 3.9.7-1),
 python3-distutils (= 3.9.9-2),
 python3-lib2to3 (= 3.9.9-2),
 python3-minimal (= 3.9.7-1),
 python3.9 (= 3.9.9-1+rpi1),
 python3.9-minimal (= 3.9.9-1+rpi1),
 readline-common (= 8.1-2),
 rpcsvc-proto (= 1.4.2-4),
 sed (= 4.8-1),
 sensible-utils (= 0.0.17),
 sysvinit-utils (= 3.00-1),
 tar (= 1.34+dfsg-1),
 tzdata (= 2021e-1),
 util-linux (= 2.37.2-4),
 xz-utils (= 5.2.5-2),
 zlib1g (= 1:1.2.11.dfsg-2)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1638735415"


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


centrifuge-dbgsym_1.0.3-10_armhf.deb
------------------------------------

 new Debian package, version 2.0.
 size 3402288 bytes: control archive=692 bytes.
     467 bytes,    12 lines      control              
     408 bytes,     4 lines      md5sums              
 Package: centrifuge-dbgsym
 Source: centrifuge
 Version: 1.0.3-10
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3484
 Depends: centrifuge (= 1.0.3-10)
 Section: debug
 Priority: optional
 Description: debug symbols for centrifuge
 Build-Ids: 4f10f4371cde5efd27b6d7610f4cdeb53a20801d 6cb51870b73bf782661916d3a13b5d038f0a6c62 ef7b2006ff7ce413f66c848c181483b432c0c275

drwxr-xr-x root/root         0 2021-12-05 20:16 ./
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/debug/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/debug/.build-id/4f/
-rw-r--r-- root/root    797044 2021-12-05 20:16 ./usr/lib/debug/.build-id/4f/10f4371cde5efd27b6d7610f4cdeb53a20801d.debug
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/debug/.build-id/6c/
-rw-r--r-- root/root    959940 2021-12-05 20:16 ./usr/lib/debug/.build-id/6c/b51870b73bf782661916d3a13b5d038f0a6c62.debug
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/debug/.build-id/ef/
-rw-r--r-- root/root   1546980 2021-12-05 20:16 ./usr/lib/debug/.build-id/ef/7b2006ff7ce413f66c848c181483b432c0c275.debug
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root    246860 2021-12-05 20:16 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/centrifuge.debug
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/share/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/share/doc/
lrwxrwxrwx root/root         0 2021-12-05 20:16 ./usr/share/doc/centrifuge-dbgsym -> centrifuge


centrifuge_1.0.3-10_armhf.deb
-----------------------------

 new Debian package, version 2.0.
 size 464268 bytes: control archive=1796 bytes.
    1168 bytes,    21 lines      control              
    2253 bytes,    30 lines      md5sums              
 Package: centrifuge
 Version: 1.0.3-10
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1377
 Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 11), python3:any, python3, hisat2, jellyfish
 Section: science
 Priority: optional
 Homepage: https://ccb.jhu.edu/software/centrifuge/
 Description: rapid and memory-efficient system for classification of DNA sequences
  Centrifuge is a very rapid and memory-efficient system for the
  classification of DNA sequences from microbial samples, with better
  sensitivity than and comparable accuracy to other leading systems. The
  system uses a novel indexing scheme based on the Burrows-Wheeler
  transform (BWT) and the Ferragina-Manzini (FM) index, optimized
  specifically for the metagenomic classification problem. Centrifuge
  requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial
  genomes) yet provides very fast classification speed, allowing it to
  process a typical DNA sequencing run within an hour. Together these
  advances enable timely and accurate analysis of large metagenomics data
  sets on conventional desktop computers.

drwxr-xr-x root/root         0 2021-12-05 20:16 ./
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/bin/
-rwxr-xr-x root/root       312 2021-12-05 20:16 ./usr/bin/centrifuge
lrwxrwxrwx root/root         0 2021-12-05 20:16 ./usr/bin/centrifuge-build -> centrifuge
lrwxrwxrwx root/root         0 2021-12-05 20:16 ./usr/bin/centrifuge-compress -> centrifuge
lrwxrwxrwx root/root         0 2021-12-05 20:16 ./usr/bin/centrifuge-download -> centrifuge
lrwxrwxrwx root/root         0 2021-12-05 20:16 ./usr/bin/centrifuge-inspect -> centrifuge
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/centrifuge/
-rwxr-xr-x root/root     19883 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge
-rwxr-xr-x root/root     12126 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-BuildSharedSequence.pl
-rwxr-xr-x root/root       407 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-RemoveEmptySequence.pl
-rwxr-xr-x root/root      1007 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-RemoveN.pl
-rwxr-xr-x root/root      2312 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-build
-rwxr-xr-x root/root    381564 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-build-bin
-rwxr-xr-x root/root    508648 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-class
-rwxr-xr-x root/root     13305 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-compress.pl
-rwxr-xr-x root/root     11670 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-download
-rwxr-xr-x root/root      1868 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-inspect
-rwxr-xr-x root/root    292612 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-inspect-bin
-rwxr-xr-x root/root      5231 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-kreport
-rwxr-xr-x root/root      3214 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-sort-nt.pl
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/centrifuge/share/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/centrifuge/share/centrifuge/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/lib/centrifuge/share/centrifuge/indices/
-rw-r--r-- root/root     12887 2021-12-05 20:16 ./usr/lib/centrifuge/share/centrifuge/indices/Makefile
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/share/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/share/doc/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/share/doc/centrifuge/
-rw-r--r-- root/root      1216 2021-12-05 20:16 ./usr/share/doc/centrifuge/changelog.Debian.gz
-rw-r--r-- root/root      1054 2021-12-05 20:16 ./usr/share/doc/centrifuge/copyright
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/
-rw-r--r-- root/root      1234 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/add.css
-rw-r--r-- root/root      1158 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/faq.shtml
-rw-r--r-- root/root       423 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/footer.inc.html
-rw-r--r-- root/root      2388 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/index.shtml.gz
-rw-r--r-- root/root     84288 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/manual.html
-rw-r--r-- root/root      1068 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/manual.shtml
-rw-r--r-- root/root      1348 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/sidebar.inc.shtml.gz
-rw-r--r-- root/root      7942 2021-12-05 20:16 ./usr/share/doc/centrifuge/html/style.css
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/share/man/
drwxr-xr-x root/root         0 2021-12-05 20:16 ./usr/share/man/man1/
-rw-r--r-- root/root      1204 2021-12-05 20:16 ./usr/share/man/man1/centrifuge-build.1.gz
-rw-r--r-- root/root       379 2021-12-05 20:16 ./usr/share/man/man1/centrifuge-compress.1.gz
-rw-r--r-- root/root       854 2021-12-05 20:16 ./usr/share/man/man1/centrifuge-download.1.gz
-rw-r--r-- root/root       920 2021-12-05 20:16 ./usr/share/man/man1/centrifuge-inspect.1.gz
-rw-r--r-- root/root      1931 2021-12-05 20:16 ./usr/share/man/man1/centrifuge.1.gz


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


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

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

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

Build Architecture: armhf
Build Type: any
Build-Space: 32944
Build-Time: 180
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 327
Job: centrifuge_1.0.3-10
Machine Architecture: armhf
Package: centrifuge
Package-Time: 539
Source-Version: 1.0.3-10
Space: 32944
Status: successful
Version: 1.0.3-10
--------------------------------------------------------------------------------
Finished at 2021-12-11T05:17:31Z
Build needed 00:08:59, 32944k disk space