Raspbian Package Auto-Building

Build log for centrifuge (1.0.3-11+b2) on armhf

centrifuge → 1.0.3-11+b2 → armhf → 2024-01-19 18:09:28 

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

+==============================================================================+
| centrifuge 1.0.3-11+b2 (armhf)               Fri, 19 Jan 2024 17:57:07 +0000 |
+==============================================================================+

Package: centrifuge
Version: 1.0.3-11+b2
Source Version: 1.0.3-11
Distribution: trixie-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/trixie-staging-armhf-sbuild-ab808f6c-2dcf-4fe4-b0c4-24d14e0d8caf' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/centrifuge-j9mnCD/resolver-Wj2AWZ' with '<<RESOLVERDIR>>'

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

Get:1 http://172.17.4.1/private trixie-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private trixie-staging/main Sources [14.4 MB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf Packages [15.0 MB]
Fetched 29.4 MB in 11s (2651 kB/s)
Reading package lists...
W: http://172.17.4.1/private/dists/trixie-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.

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


Check APT
---------

Checking available source versions...

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

Reading package lists...
NOTICE: '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 719 kB of source archives.
Get:1 http://172.17.4.1/private trixie-staging/main centrifuge 1.0.3-11 (dsc) [2037 B]
Get:2 http://172.17.4.1/private trixie-staging/main centrifuge 1.0.3-11 (tar) [701 kB]
Get:3 http://172.17.4.1/private trixie-staging/main centrifuge 1.0.3-11 (diff) [15.2 kB]
Fetched 719 kB in 0s (4053 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/centrifuge-j9mnCD/centrifuge-1.0.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/centrifuge-j9mnCD' 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 [476 B]
Fetched 1829 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 packages were automatically installed and are no longer required:
  krb5-locales libpam-cap util-linux-extra
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils bsdutils debhelper
  dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
  gettext-base groff-base intltool-debian jellyfish libarchive-zip-perl
  libblkid1 libbrotli1 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1
  libexpat1 libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu72
  libjellyfish-2.0-2 libmagic-mgc libmagic1 libmount1 libnghttp2-14
  libpipeline1 libpsl5 libpython3-stdlib libpython3.11-minimal
  libpython3.11-stdlib librtmp1 libsmartcols1 libssh2-1 libsub-override-perl
  libtool libuchardet0 libuuid1 libxml2 m4 man-db media-types mount netbase
  po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
  python3-pkg-resources python3-setuptools python3.11 python3.11-minimal
  util-linux util-linux-extra
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
  python3-installer python3-wheel gettext-doc libasprintf-dev libgettextpo-dev
  groff cryptsetup-bin libtool-doc gfortran | fortran95-compiler gcj-jdk
  m4-doc apparmor less www-browser nfs-common libmail-box-perl python3-doc
  python3-tk python3-venv python-setuptools-doc python3.11-venv python3.11-doc
  binfmt-support dosfstools kbd util-linux-locales
Recommended packages:
  curl | wget | lynx ca-certificates libarchive-cpio-perl publicsuffix
  libltdl-dev uuid-runtime libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev bsdextrautils debhelper
  dh-autoreconf dh-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 libicu72
  libjellyfish-2.0-2 libmagic-mgc libmagic1 libnghttp2-14 libpipeline1 libpsl5
  libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib librtmp1
  libssh2-1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db
  media-types netbase po-debconf python3 python3-distutils python3-lib2to3
  python3-minimal python3-pkg-resources python3-setuptools python3.11
  python3.11-minimal sbuild-build-depends-main-dummy
The following packages will be upgraded:
  bsdutils libblkid1 libmount1 libsmartcols1 libuuid1 mount util-linux
  util-linux-extra
8 upgraded, 56 newly installed, 0 to remove and 40 not upgraded.
Need to get 28.2 MB of archives.
After this operation, 101 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [900 B]
Get:2 http://172.17.4.1/private trixie-staging/main armhf bsdutils armhf 1:2.39.3-6 [87.1 kB]
Get:3 http://172.17.4.1/private trixie-staging/main armhf libsmartcols1 armhf 2.39.3-6 [102 kB]
Get:4 http://172.17.4.1/private trixie-staging/main armhf util-linux-extra armhf 2.39.3-6 [135 kB]
Get:5 http://172.17.4.1/private trixie-staging/main armhf util-linux armhf 2.39.3-6 [1113 kB]
Get:6 http://172.17.4.1/private trixie-staging/main armhf mount armhf 2.39.3-6 [134 kB]
Get:7 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-minimal armhf 3.11.7-2 [801 kB]
Get:8 http://172.17.4.1/private trixie-staging/main armhf libexpat1 armhf 2.5.0-2 [76.8 kB]
Get:9 http://172.17.4.1/private trixie-staging/main armhf python3.11-minimal armhf 3.11.7-2 [1677 kB]
Get:10 http://172.17.4.1/private trixie-staging/main armhf python3-minimal armhf 3.11.4-5 [26.2 kB]
Get:11 http://172.17.4.1/private trixie-staging/main armhf media-types all 10.1.0 [26.9 kB]
Get:12 http://172.17.4.1/private trixie-staging/main armhf netbase all 6.4 [12.8 kB]
Get:13 http://172.17.4.1/private trixie-staging/main armhf libuuid1 armhf 2.39.3-6 [28.3 kB]
Get:14 http://172.17.4.1/private trixie-staging/main armhf libpython3.11-stdlib armhf 3.11.7-2 [1694 kB]
Get:15 http://172.17.4.1/private trixie-staging/main armhf python3.11 armhf 3.11.7-2 [590 kB]
Get:16 http://172.17.4.1/private trixie-staging/main armhf libpython3-stdlib armhf 3.11.4-5 [9200 B]
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Get:18 http://172.17.4.1/private trixie-staging/main armhf libblkid1 armhf 2.39.3-6 [145 kB]
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Get:20 http://172.17.4.1/private trixie-staging/main armhf libuchardet0 armhf 0.0.8-1 [65.5 kB]
Get:21 http://172.17.4.1/private trixie-staging/main armhf groff-base armhf 1.23.0-3 [1033 kB]
Get:22 http://172.17.4.1/private trixie-staging/main armhf bsdextrautils armhf 2.39.3-6 [81.4 kB]
Get:23 http://172.17.4.1/private trixie-staging/main armhf libpipeline1 armhf 1.5.7-1 [33.4 kB]
Get:24 http://172.17.4.1/private trixie-staging/main armhf man-db armhf 2.12.0-3 [1358 kB]
Get:25 http://172.17.4.1/private trixie-staging/main armhf libmagic-mgc armhf 1:5.45-2 [314 kB]
Get:26 http://172.17.4.1/private trixie-staging/main armhf libmagic1 armhf 1:5.45-2 [96.1 kB]
Get:27 http://172.17.4.1/private trixie-staging/main armhf file armhf 1:5.45-2 [41.6 kB]
Get:28 http://172.17.4.1/private trixie-staging/main armhf gettext-base armhf 0.21-14 [157 kB]
Get:29 http://172.17.4.1/private trixie-staging/main armhf m4 armhf 1.4.19-4 [256 kB]
Get:30 http://172.17.4.1/private trixie-staging/main armhf autoconf all 2.71-3 [332 kB]
Get:31 http://172.17.4.1/private trixie-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:32 http://172.17.4.1/private trixie-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:33 http://172.17.4.1/private trixie-staging/main armhf autopoint all 0.21-14 [496 kB]
Get:34 http://172.17.4.1/private trixie-staging/main armhf libdebhelper-perl all 13.11.9 [82.3 kB]
Get:35 http://172.17.4.1/private trixie-staging/main armhf libtool all 2.4.7-7 [517 kB]
Get:36 http://172.17.4.1/private trixie-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:37 http://172.17.4.1/private trixie-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:38 http://172.17.4.1/private trixie-staging/main armhf libsub-override-perl all 0.10-1 [10.6 kB]
Get:39 http://172.17.4.1/private trixie-staging/main armhf libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:40 http://172.17.4.1/private trixie-staging/main armhf dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:41 http://172.17.4.1/private trixie-staging/main armhf libelf1 armhf 0.188-2.1+rpi1 [171 kB]
Get:42 http://172.17.4.1/private trixie-staging/main armhf dwz armhf 0.15-1 [92.4 kB]
Get:43 http://172.17.4.1/private trixie-staging/main armhf libicu72 armhf 72.1-4 [9009 kB]
Get:44 http://172.17.4.1/private trixie-staging/main armhf libxml2 armhf 2.9.14+dfsg-1.3 [571 kB]
Get:45 http://172.17.4.1/private trixie-staging/main armhf gettext armhf 0.21-14 [1203 kB]
Get:46 http://172.17.4.1/private trixie-staging/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:47 http://172.17.4.1/private trixie-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:48 http://172.17.4.1/private trixie-staging/main armhf debhelper all 13.11.9 [956 kB]
Get:49 http://172.17.4.1/private trixie-staging/main armhf python3-lib2to3 all 3.11.5-1 [77.5 kB]
Get:50 http://172.17.4.1/private trixie-staging/main armhf python3-distutils all 3.11.5-1 [131 kB]
Get:51 http://172.17.4.1/private trixie-staging/main armhf python3-pkg-resources all 68.1.2-2 [241 kB]
Get:52 http://172.17.4.1/private trixie-staging/main armhf python3-setuptools all 68.1.2-2 [468 kB]
Get:53 http://172.17.4.1/private trixie-staging/main armhf dh-python all 6.20231223 [108 kB]
Get:54 http://172.17.4.1/private trixie-staging/main armhf libbrotli1 armhf 1.1.0-2 [280 kB]
Get:55 http://172.17.4.1/private trixie-staging/main armhf libnghttp2-14 armhf 1.58.0-1 [61.7 kB]
Get:56 http://172.17.4.1/private trixie-staging/main armhf libpsl5 armhf 0.21.2-1+b1 [57.8 kB]
Get:57 http://172.17.4.1/private trixie-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:58 http://172.17.4.1/private trixie-staging/main armhf libssh2-1 armhf 1.11.0-4 [195 kB]
Get:59 http://172.17.4.1/private trixie-staging/main armhf libcurl3-gnutls armhf 8.5.0-2+rpi1 [372 kB]
Get:60 http://172.17.4.1/private trixie-staging/main armhf libdeflate0 armhf 1.18-1 [38.3 kB]
Get:61 http://172.17.4.1/private trixie-staging/main armhf libhtscodecs2 armhf 1.6.0-1 [60.3 kB]
Get:62 http://172.17.4.1/private trixie-staging/main armhf libhts3 armhf 1.18+ds-1 [380 kB]
Get:63 http://172.17.4.1/private trixie-staging/main armhf libjellyfish-2.0-2 armhf 2.3.1-2 [57.5 kB]
Get:64 http://172.17.4.1/private trixie-staging/main armhf jellyfish armhf 2.3.1-2 [622 kB]
debconf: delaying package configuration, since apt-utils is not installed
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(Reading database ... 14716 files and directories currently installed.)
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Setting up libhtscodecs2:armhf (1.6.0-1) ...
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Setting up libpsl5:armhf (0.21.2-1+b1) ...
Setting up libicu72:armhf (72.1-4) ...
Setting up bsdextrautils (2.39.3-6) ...
Setting up libmagic-mgc (1:5.45-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libdebhelper-perl (13.11.9) ...
Setting up libbrotli1:armhf (1.1.0-2) ...
Setting up libnghttp2-14:armhf (1.58.0-1) ...
Setting up libmagic1:armhf (1:5.45-2) ...
Setting up libdeflate0:armhf (1.18-1) ...
Setting up gettext-base (0.21-14) ...
Setting up m4 (1.4.19-4) ...
Setting up file (1:5.45-2) ...
Setting up libjellyfish-2.0-2:armhf (2.3.1-2) ...
Setting up autotools-dev (20220109.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up autopoint (0.21-14) ...
Setting up autoconf (2.71-3) ...
Setting up mount (2.39.3-6) ...
Setting up libuchardet0:armhf (0.0.8-1) ...
Setting up libsub-override-perl (0.10-1) ...
Setting up libssh2-1:armhf (1.11.0-4) ...
Setting up netbase (6.4) ...
Setting up libelf1:armhf (0.188-2.1+rpi1) ...
Setting up libxml2:armhf (2.9.14+dfsg-1.3) ...
Setting up util-linux-extra (2.39.3-6) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.1-1) ...
Setting up gettext (0.21-14) ...
Setting up libtool (2.4.7-7) ...
Setting up libpython3.11-stdlib:armhf (3.11.7-2) ...
Setting up libcurl3-gnutls:armhf (8.5.0-2+rpi1) ...
Setting up intltool-debian (0.35.0+20060710.6) ...
Setting up dh-autoreconf (20) ...
Setting up dh-strip-nondeterminism (1.13.1-1) ...
Setting up dwz (0.15-1) ...
Setting up groff-base (1.23.0-3) ...
Setting up libpython3-stdlib:armhf (3.11.4-5) ...
Setting up python3.11 (3.11.7-2) ...
Setting up libhts3:armhf (1.18+ds-1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up python3 (3.11.4-5) ...
Setting up man-db (2.12.0-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up jellyfish (2.3.1-2) ...
Setting up python3-lib2to3 (3.11.5-1) ...
Setting up python3-pkg-resources (68.1.2-2) ...
Setting up python3-distutils (3.11.5-1) ...
Setting up python3-setuptools (68.1.2-2) ...
Setting up debhelper (13.11.9) ...
Setting up dh-python (6.20231223) ...
Setting up sbuild-build-depends-main-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.37-12+rpi2) ...

+------------------------------------------------------------------------------+
| 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_2.41-6+rpi1 dpkg-dev_1.22.1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc-12_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 libc6-dev_2.37-12+rpi2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 linux-libc-dev_6.5.6-1+rpi1
Package versions: adduser_3.137 apt_2.7.6 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13+rpi1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.41-6+rpi1 binutils-arm-linux-gnueabihf_2.41-6+rpi1 binutils-common_2.41-6+rpi1 bsdextrautils_2.39.3-6 bsdutils_1:2.39.3-6 build-essential_12.10 bzip2_1.0.8-5+b2 coreutils_9.1-1 cpp_4:13.2.0-1+rpi1 cpp-12_12.3.0-13+rpi1 cpp-13_13.2.0-7+rpi1 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.9 debianutils_5.14 dh-autoreconf_20 dh-python_6.20231223 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dirmngr_2.2.40-1.1 dpkg_1.22.1+rpi1 dpkg-dev_1.22.1+rpi1 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.32.2-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1+rpi1 g++-12_12.3.0-13+rpi1 g++-13_13.2.0-7+rpi1 gcc_4:13.2.0-1+rpi1 gcc-12_12.3.0-13+rpi1 gcc-12-base_12.3.0-13+rpi1 gcc-13_13.2.0-7+rpi1 gcc-13-base_13.2.0-7+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-14 gettext-base_0.21-14 gnupg_2.2.40-1.1 gnupg-l10n_2.2.40-1.1 gnupg-utils_2.2.40-1.1 gpg_2.2.40-1.1 gpg-agent_2.2.40-1.1 gpg-wks-client_2.2.40-1.1 gpg-wks-server_2.2.40-1.1 gpgconf_2.2.40-1.1 gpgsm_2.2.40-1.1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-3 gzip_1.12-1 hostname_3.23+nmu1 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 iputils-ping_3:20221126-1 jellyfish_2.3.1-2 krb5-locales_1.20.1-5 libacl1_2.3.1-3 libapt-pkg6.0_2.7.6 libarchive-zip-perl_1.68-1 libasan8_13.2.0-7+rpi1 libassuan0_2.5.6-1 libatomic1_13.2.0-7+rpi1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.2-1 libaudit1_1:3.1.2-1 libbinutils_2.41-6+rpi1 libblkid1_2.39.3-6 libbrotli1_1.1.0-2 libbz2-1.0_1.0.8-5+b2 libc-bin_2.37-12+rpi2 libc-dev-bin_2.37-12+rpi2 libc6_2.37-12+rpi2 libc6-dev_2.37-12+rpi2 libcap-ng0_0.8.3-3 libcap2_1:2.66-4 libcap2-bin_1:2.66-4 libcc1-0_13.2.0-7+rpi1 libcom-err2_1.47.0-2 libcrypt-dev_1:4.4.36-2 libcrypt1_1:4.4.36-2 libctf-nobfd0_2.41-6+rpi1 libctf0_2.41-6+rpi1 libcurl3-gnutls_8.5.0-2+rpi1 libdb5.3_5.3.28+dfsg2-4 libdebconfclient0_0.271 libdebhelper-perl_13.11.9 libdeflate0_1.18-1 libdpkg-perl_1.22.1+rpi1 libelf1_0.188-2.1+rpi1 libexpat1_2.5.0-2 libext2fs2_1.47.0-2 libfakeroot_1.32.2-1 libffi8_3.4.4-2 libfile-find-rule-perl_0.34-3 libfile-stripnondeterminism-perl_1.13.1-1 libgcc-12-dev_12.3.0-13+rpi1 libgcc-13-dev_13.2.0-7+rpi1 libgcc-s1_13.2.0-7+rpi1 libgcrypt20_1.10.3-2 libgdbm-compat4_1.23-5 libgdbm6_1.23-5 libgmp10_2:6.3.0+dfsg-2 libgnutls30_3.8.2-1 libgomp1_13.2.0-7+rpi1 libgpg-error0_1.47-3 libgssapi-krb5-2_1.20.1-5 libhogweed6_3.9.1-2 libhts3_1.18+ds-1 libhtscodecs2_1.6.0-1 libicu72_72.1-4 libidn2-0_2.3.4-1 libisl23_0.26-3 libjansson4_2.14-2 libjellyfish-2.0-2_2.3.1-2 libk5crypto3_1.20.1-5 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-5 libkrb5support0_1.20.1-5 libksba8_1.6.5-2 libldap-2.5-0_2.5.13+dfsg-5+rpi1 liblz4-1_1.9.4-1+rpi1+b1 liblzma5_5.4.5-0.1 libmagic-mgc_1:5.45-2 libmagic1_1:5.45-2 libmd0_1.1.0-1 libmount1_2.39.3-6 libmpc3_1.3.1-1 libmpfr6_4.2.1-1 libncursesw6_6.4+20231209-1 libnettle8_3.9.1-2 libnghttp2-14_1.58.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-3 libnsl2_1.3.0-3 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-2 libpam-cap_1:2.66-4 libpam-modules_1.5.2-9.1 libpam-modules-bin_1.5.2-9.1 libpam-runtime_1.5.2-9.1 libpam0g_1.5.2-9.1 libpcre2-8-0_10.42-4 libpcre3_2:8.39-15 libperl5.32_5.32.1-6 libperl5.36_5.36.0-10 libpipeline1_1.5.7-1 libpsl5_0.21.2-1+b1 libpython3-stdlib_3.11.4-5 libpython3.11-minimal_3.11.7-2 libpython3.11-stdlib_3.11.7-2 libreadline8_8.2-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg1-4 libsasl2-modules-db_2.1.28+dfsg1-4 libseccomp2_2.5.4-2+rpi1 libselinux1_3.5-1 libsemanage-common_3.5-1 libsemanage2_3.5-1 libsepol1_3.1-1 libsepol2_3.5-2 libsframe1_2.41-6+rpi1 libsmartcols1_2.39.3-6 libsqlite3-0_3.44.2-1 libss2_1.47.0-2 libssh2-1_1.11.0-4 libssl1.1_1.1.1o-1 libssl3_3.1.4-2 libstdc++-12-dev_12.3.0-13+rpi1 libstdc++-13-dev_13.2.0-7+rpi1 libstdc++6_13.2.0-7+rpi1 libsub-override-perl_0.10-1 libsystemd0_254.5-1+rpi1 libtasn1-6_4.19.0-3 libtext-glob-perl_0.11-3 libtinfo6_6.4+20231209-1 libtirpc-common_1.3.4+ds-1 libtirpc-dev_1.3.4+ds-1 libtirpc3_1.3.4+ds-1 libtool_2.4.7-7 libubsan1_13.2.0-7+rpi1 libuchardet0_0.0.8-1 libudev1_254.5-1+rpi1 libunistring2_1.0-2 libunistring5_1.1-2 libuuid1_2.39.3-6 libxml2_2.9.14+dfsg-1.3 libxxhash0_0.8.2-2 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.5.6-1+rpi1 login_1:4.13+dfsg1-3 logsave_1.47.0-2 lsb-base_11.6+rpi1 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.0-3 mawk_1.3.4.20231126-1 media-types_10.1.0 mount_2.39.3-6 nano_7.2-1 ncurses-base_6.4+20231209-1 ncurses-bin_6.4+20231209-1 netbase_6.4 passwd_1:4.13+dfsg1-3 patch_2.7.6-7 perl_5.36.0-10 perl-base_5.36.0-10 perl-modules-5.32_5.32.1-6 perl-modules-5.36_5.36.0-10 pinentry-curses_1.2.1-3 po-debconf_1.0.21+nmu1 python3_3.11.4-5 python3-distutils_3.11.5-1 python3-lib2to3_3.11.5-1 python3-minimal_3.11.4-5 python3-pkg-resources_68.1.2-2 python3-setuptools_68.1.2-2 python3.11_3.11.7-2 python3.11-minimal_3.11.7-2 raspbian-archive-keyring_20120528.2 readline-common_8.2-3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.20 sysvinit-utils_3.08-5 tar_1.34+dfsg-1.3 tzdata_2023c-11 usrmerge_38 util-linux_2.39.3-6 util-linux-extra_2.39.3-6 xz-utils_5.4.5-0.1 zlib1g_1:1.2.13.dfsg-3

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


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

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

Format: 3.0 (quilt)
Source: centrifuge
Binary: centrifuge
Architecture: any
Version: 1.0.3-11
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: 4.6.1
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
 8be8e53beb61d1f6a4b681b1e383999e99bde55d 15220 centrifuge_1.0.3-11.debian.tar.xz
Checksums-Sha256:
 71340f5c0c20dd4f7c4d98ea87f9edcbb1443fff8434e816a5465cbebaca9343 701273 centrifuge_1.0.3.orig.tar.gz
 bdf867738f93e51112837a45b213b0fb3be9950bda5062f9cd179f9f348d5429 15220 centrifuge_1.0.3-11.debian.tar.xz
Files:
 4ab20730ae43f26a98b754d83213e10c 701273 centrifuge_1.0.3.orig.tar.gz
 2e0e361b6c2198258d63e58f6cc8758e 15220 centrifuge_1.0.3-11.debian.tar.xz

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gpgv: Signature made Mon Oct 10 05:56:45 2022 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./centrifuge_1.0.3-11.dsc: no acceptable signature found
dpkg-source: info: extracting centrifuge in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking centrifuge_1.0.3.orig.tar.gz
dpkg-source: info: unpacking centrifuge_1.0.3-11.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying 0001-Makefile-Use-consistent-build-time-and-build-host.patch
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

Hack binNMU version
-------------------

Created changelog entry for binNMU version 1.0.3-11+b2

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=7507367173ad4858a061fdd2cf60741a
JOURNAL_STREAM=8:39174
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=trixie-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=trixie-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=117
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=trixie-staging-armhf-sbuild-ab808f6c-2dcf-4fe4-b0c4-24d14e0d8caf
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_CLASS=background
XDG_SESSION_ID=c77128
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 1.0.3-11+b2
dpkg-buildpackage: info: source distribution trixie-staging
 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="\"BUILDHOST\"" -DBUILD_TIME="\"`date --utc --date=@1705687582 +%F`\"" -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 -fstack-clash-protection -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="\"BUILDHOST\"" -DBUILD_TIME="\"`date --utc --date=@1705687582 +%F`\"" -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 -fstack-clash-protection -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="\"BUILDHOST\"" -DBUILD_TIME="\"`date --utc --date=@1705687582 +%F`\"" -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 -fstack-clash-protection -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;
      |                                                                   ^~~~~
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;
      |                                                                   ^~~~~
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:
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);
      |                                                                      ^~~~~~~~
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);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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);
      |                                        ^~~~~~~~
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 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);
      |                                                              ^~~~~~~~
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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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++) {
      |                         ~~^~~~~~~~~~~
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]
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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]
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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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);
      |                 ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]
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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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);
      |                 ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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);
      |                                                                      ^~~~~~~~
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: 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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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:
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);
      |                                                                      ^~~~~~~~
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]);
      |                                                      ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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);
      |                                                                      ^~~~~~~~
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} ;
      |                ^~~
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 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:
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);
      |                                                                      ^~~~~~~~
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);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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++/13/set:62,
                 from centrifuge_inspect.cpp:24:
/usr/include/c++/13/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(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++/13/bits/stl_tree.h:2458:7: 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
 2458 |       _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
      |       ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/13/map:63,
                 from bt2_idx.h:34:
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = 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> >]’,
    inlined from ‘Ebwt<index_t>::Ebwt(const std::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]’ at bt2_idx.h:702:28:
/usr/include/c++/13/bits/stl_map.h:513:44: 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
  513 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  514 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  515 |                                             std::tuple<>());
      |                                             ~~~~~~~~~~~~~~~
In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = 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> >]’,
    inlined from ‘Ebwt<index_t>::Ebwt(const std::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]’ at bt2_idx.h:743:36:
/usr/include/c++/13/bits/stl_map.h:513:44: 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
  513 |           __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
      |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  514 |                                             std::tuple<const key_type&>(__k),
      |                                             ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  515 |                                             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;
      |                                                                   ^~~~~
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:
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);
      |                                                                      ^~~~~~~~
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);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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;
      |                                                                   ^~~~~
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:
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);
      |                                                                      ^~~~~~~~
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);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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 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;
      |                                                                   ^~~~~
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);
      |                                        ^~~~~~~~
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]
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:
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);
      |                                                                      ^~~~~~~~
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);
      |                         ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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-inspect-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-build-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-inspect-bin debian/centrifuge/usr/lib/centrifuge/centrifuge-build-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_1.0.3-11+b2_armhf.deb'.
dpkg-deb: building package 'centrifuge-dbgsym' in '../centrifuge-dbgsym_1.0.3-11+b2_armhf.deb'.
 dpkg-genbuildinfo --build=any -O../centrifuge_1.0.3-11+b2_armhf.buildinfo
 dpkg-genchanges --build=any -mRaspbian pi4 based autobuilder <root@raspbian.org> -O../centrifuge_1.0.3-11+b2_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 2024-01-19T18:09:19Z

Finished
--------

I: Built successfully

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


centrifuge_1.0.3-11+b2_armhf.changes:
-------------------------------------

Format: 1.8
Date: Fri, 19 Jan 2024 18:06:22 +0000
Source: centrifuge (1.0.3-11)
Binary: centrifuge centrifuge-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.0.3-11+b2
Distribution: trixie-staging
Urgency: low
Maintainer: Raspbian pi4 based autobuilder <root@raspbian.org>
Changed-By: Raspbian pi4 based autobuilder <root@raspbian.org>
Description:
 centrifuge - rapid and memory-efficient system for classification of DNA seque
Changes:
 centrifuge (1.0.3-11+b2) trixie-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
Checksums-Sha1:
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 15e8e652d1b48075e1cd33c903819734bbd67374 466812 centrifuge_1.0.3-11+b2_armhf.deb
Checksums-Sha256:
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 255ce18d7d7ea72c2730a7d53942d9d30256614d0579bdab9515dbff033205fb 6734 centrifuge_1.0.3-11+b2_armhf.buildinfo
 625555ad0626fea967f534fc01703dfdf3b75ee05114d4cf70e50bd0ad2615cf 466812 centrifuge_1.0.3-11+b2_armhf.deb
Files:
 9ae0cdd1a4ebe64eac1be0dfbe4b9685 3339292 debug optional centrifuge-dbgsym_1.0.3-11+b2_armhf.deb
 7c7968b4ed55060c799eb380f346e3c4 6734 science optional centrifuge_1.0.3-11+b2_armhf.buildinfo
 018262ce3465e8a94c26562a7eb0d608 466812 science optional centrifuge_1.0.3-11+b2_armhf.deb

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

Format: 1.0
Source: centrifuge (1.0.3-11)
Binary: centrifuge centrifuge-dbgsym
Architecture: armhf
Version: 1.0.3-11+b2
Binary-Only-Changes:
 centrifuge (1.0.3-11+b2) trixie-staging; urgency=low, binary-only=yes
 .
   * Binary-only non-maintainer upload for armhf; no source changes.
   * rebuild due to debcheck failure
 .
  -- Raspbian pi4 based autobuilder <root@raspbian.org>  Fri, 19 Jan 2024 18:06:22 +0000
Checksums-Md5:
 9ae0cdd1a4ebe64eac1be0dfbe4b9685 3339292 centrifuge-dbgsym_1.0.3-11+b2_armhf.deb
 018262ce3465e8a94c26562a7eb0d608 466812 centrifuge_1.0.3-11+b2_armhf.deb
Checksums-Sha1:
 14e2e74526d06f6cdb80b8e53731c885bba66c10 3339292 centrifuge-dbgsym_1.0.3-11+b2_armhf.deb
 15e8e652d1b48075e1cd33c903819734bbd67374 466812 centrifuge_1.0.3-11+b2_armhf.deb
Checksums-Sha256:
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 625555ad0626fea967f534fc01703dfdf3b75ee05114d4cf70e50bd0ad2615cf 466812 centrifuge_1.0.3-11+b2_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Fri, 19 Jan 2024 18:09:18 +0000
Build-Path: /<<PKGBUILDDIR>>
Build-Tainted-By:
 merged-usr-via-aliased-dirs
Installed-Build-Depends:
 autoconf (= 2.71-3),
 automake (= 1:1.16.5-1.3),
 autopoint (= 0.21-14),
 autotools-dev (= 20220109.1),
 base-files (= 13+rpi1),
 base-passwd (= 3.6.3),
 bash (= 5.2.21-2),
 binutils (= 2.41-6+rpi1),
 binutils-arm-linux-gnueabihf (= 2.41-6+rpi1),
 binutils-common (= 2.41-6+rpi1),
 bsdextrautils (= 2.39.3-6),
 bsdutils (= 1:2.39.3-6),
 build-essential (= 12.10),
 bzip2 (= 1.0.8-5+b2),
 coreutils (= 9.1-1),
 cpp (= 4:13.2.0-1+rpi1),
 cpp-12 (= 12.3.0-13+rpi1),
 cpp-13 (= 13.2.0-7+rpi1),
 dash (= 0.5.12-6),
 debconf (= 1.5.82),
 debhelper (= 13.11.9),
 debianutils (= 5.14),
 dh-autoreconf (= 20),
 dh-python (= 6.20231223),
 dh-strip-nondeterminism (= 1.13.1-1),
 diffutils (= 1:3.10-1),
 dpkg (= 1.22.1+rpi1),
 dpkg-dev (= 1.22.1+rpi1),
 dwz (= 0.15-1),
 file (= 1:5.45-2),
 findutils (= 4.9.0-5),
 g++ (= 4:13.2.0-1+rpi1),
 g++-13 (= 13.2.0-7+rpi1),
 gcc (= 4:13.2.0-1+rpi1),
 gcc-12 (= 12.3.0-13+rpi1),
 gcc-12-base (= 12.3.0-13+rpi1),
 gcc-13 (= 13.2.0-7+rpi1),
 gcc-13-base (= 13.2.0-7+rpi1),
 gettext (= 0.21-14),
 gettext-base (= 0.21-14),
 grep (= 3.11-3),
 groff-base (= 1.23.0-3),
 gzip (= 1.12-1),
 hostname (= 3.23+nmu1),
 init-system-helpers (= 1.66),
 intltool-debian (= 0.35.0+20060710.6),
 jellyfish (= 2.3.1-2),
 libacl1 (= 2.3.1-3),
 libarchive-zip-perl (= 1.68-1),
 libasan8 (= 13.2.0-7+rpi1),
 libatomic1 (= 13.2.0-7+rpi1),
 libattr1 (= 1:2.5.1-4),
 libaudit-common (= 1:3.1.2-1),
 libaudit1 (= 1:3.1.2-1),
 libbinutils (= 2.41-6+rpi1),
 libblkid1 (= 2.39.3-6),
 libbrotli1 (= 1.1.0-2),
 libbz2-1.0 (= 1.0.8-5+b2),
 libc-bin (= 2.37-12+rpi2),
 libc-dev-bin (= 2.37-12+rpi2),
 libc6 (= 2.37-12+rpi2),
 libc6-dev (= 2.37-12+rpi2),
 libcap-ng0 (= 0.8.3-3),
 libcap2 (= 1:2.66-4),
 libcc1-0 (= 13.2.0-7+rpi1),
 libcom-err2 (= 1.47.0-2),
 libcrypt-dev (= 1:4.4.36-2),
 libcrypt1 (= 1:4.4.36-2),
 libctf-nobfd0 (= 2.41-6+rpi1),
 libctf0 (= 2.41-6+rpi1),
 libcurl3-gnutls (= 8.5.0-2+rpi1),
 libdb5.3 (= 5.3.28+dfsg2-4),
 libdebconfclient0 (= 0.271),
 libdebhelper-perl (= 13.11.9),
 libdeflate0 (= 1.18-1),
 libdpkg-perl (= 1.22.1+rpi1),
 libelf1 (= 0.188-2.1+rpi1),
 libexpat1 (= 2.5.0-2),
 libffi8 (= 3.4.4-2),
 libfile-find-rule-perl (= 0.34-3),
 libfile-stripnondeterminism-perl (= 1.13.1-1),
 libgcc-12-dev (= 12.3.0-13+rpi1),
 libgcc-13-dev (= 13.2.0-7+rpi1),
 libgcc-s1 (= 13.2.0-7+rpi1),
 libgcrypt20 (= 1.10.3-2),
 libgdbm-compat4 (= 1.23-5),
 libgdbm6 (= 1.23-5),
 libgmp10 (= 2:6.3.0+dfsg-2),
 libgnutls30 (= 3.8.2-1),
 libgomp1 (= 13.2.0-7+rpi1),
 libgpg-error0 (= 1.47-3),
 libgssapi-krb5-2 (= 1.20.1-5),
 libhogweed6 (= 3.9.1-2),
 libhts3 (= 1.18+ds-1),
 libhtscodecs2 (= 1.6.0-1),
 libicu72 (= 72.1-4),
 libidn2-0 (= 2.3.4-1),
 libisl23 (= 0.26-3),
 libjansson4 (= 2.14-2),
 libjellyfish-2.0-2 (= 2.3.1-2),
 libk5crypto3 (= 1.20.1-5),
 libkeyutils1 (= 1.6.3-2),
 libkrb5-3 (= 1.20.1-5),
 libkrb5support0 (= 1.20.1-5),
 libldap-2.5-0 (= 2.5.13+dfsg-5+rpi1),
 liblz4-1 (= 1.9.4-1+rpi1+b1),
 liblzma5 (= 5.4.5-0.1),
 libmagic-mgc (= 1:5.45-2),
 libmagic1 (= 1:5.45-2),
 libmd0 (= 1.1.0-1),
 libmount1 (= 2.39.3-6),
 libmpc3 (= 1.3.1-1),
 libmpfr6 (= 4.2.1-1),
 libncursesw6 (= 6.4+20231209-1),
 libnettle8 (= 3.9.1-2),
 libnghttp2-14 (= 1.58.0-1),
 libnsl-dev (= 1.3.0-3),
 libnsl2 (= 1.3.0-3),
 libnumber-compare-perl (= 0.03-3),
 libp11-kit0 (= 0.25.3-2),
 libpam-modules (= 1.5.2-9.1),
 libpam-modules-bin (= 1.5.2-9.1),
 libpam-runtime (= 1.5.2-9.1),
 libpam0g (= 1.5.2-9.1),
 libpcre2-8-0 (= 10.42-4),
 libperl5.36 (= 5.36.0-10),
 libpipeline1 (= 1.5.7-1),
 libpsl5 (= 0.21.2-1+b1),
 libpython3-stdlib (= 3.11.4-5),
 libpython3.11-minimal (= 3.11.7-2),
 libpython3.11-stdlib (= 3.11.7-2),
 libreadline8 (= 8.2-3),
 librtmp1 (= 2.4+20151223.gitfa8646d.1-2+b2),
 libsasl2-2 (= 2.1.28+dfsg1-4),
 libsasl2-modules-db (= 2.1.28+dfsg1-4),
 libseccomp2 (= 2.5.4-2+rpi1),
 libselinux1 (= 3.5-1),
 libsframe1 (= 2.41-6+rpi1),
 libsmartcols1 (= 2.39.3-6),
 libsqlite3-0 (= 3.44.2-1),
 libssh2-1 (= 1.11.0-4),
 libssl3 (= 3.1.4-2),
 libstdc++-13-dev (= 13.2.0-7+rpi1),
 libstdc++6 (= 13.2.0-7+rpi1),
 libsub-override-perl (= 0.10-1),
 libsystemd0 (= 254.5-1+rpi1),
 libtasn1-6 (= 4.19.0-3),
 libtext-glob-perl (= 0.11-3),
 libtinfo6 (= 6.4+20231209-1),
 libtirpc-common (= 1.3.4+ds-1),
 libtirpc-dev (= 1.3.4+ds-1),
 libtirpc3 (= 1.3.4+ds-1),
 libtool (= 2.4.7-7),
 libubsan1 (= 13.2.0-7+rpi1),
 libuchardet0 (= 0.0.8-1),
 libudev1 (= 254.5-1+rpi1),
 libunistring5 (= 1.1-2),
 libuuid1 (= 2.39.3-6),
 libxml2 (= 2.9.14+dfsg-1.3),
 libzstd1 (= 1.5.5+dfsg2-2),
 linux-libc-dev (= 6.5.6-1+rpi1),
 login (= 1:4.13+dfsg1-3),
 m4 (= 1.4.19-4),
 make (= 4.3-4.1),
 man-db (= 2.12.0-3),
 mawk (= 1.3.4.20231126-1),
 media-types (= 10.1.0),
 ncurses-base (= 6.4+20231209-1),
 ncurses-bin (= 6.4+20231209-1),
 netbase (= 6.4),
 patch (= 2.7.6-7),
 perl (= 5.36.0-10),
 perl-base (= 5.36.0-10),
 perl-modules-5.36 (= 5.36.0-10),
 po-debconf (= 1.0.21+nmu1),
 python3 (= 3.11.4-5),
 python3-distutils (= 3.11.5-1),
 python3-lib2to3 (= 3.11.5-1),
 python3-minimal (= 3.11.4-5),
 python3-pkg-resources (= 68.1.2-2),
 python3-setuptools (= 68.1.2-2),
 python3.11 (= 3.11.7-2),
 python3.11-minimal (= 3.11.7-2),
 readline-common (= 8.2-3),
 rpcsvc-proto (= 1.4.3-1),
 sed (= 4.9-1),
 sensible-utils (= 0.0.20),
 sysvinit-utils (= 3.08-5),
 tar (= 1.34+dfsg-1.3),
 tzdata (= 2023c-11),
 usrmerge (= 38),
 util-linux (= 2.39.3-6),
 xz-utils (= 5.4.5-0.1),
 zlib1g (= 1:1.2.13.dfsg-3)
Environment:
 DEB_BUILD_OPTIONS="parallel=4"
 LANG="en_GB.UTF-8"
 LC_ALL="C.UTF-8"
 SOURCE_DATE_EPOCH="1705687582"


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


centrifuge-dbgsym_1.0.3-11+b2_armhf.deb
---------------------------------------

 new Debian package, version 2.0.
 size 3339292 bytes: control archive=700 bytes.
     484 bytes,    12 lines      control
     408 bytes,     4 lines      md5sums
 Package: centrifuge-dbgsym
 Source: centrifuge (1.0.3-11)
 Version: 1.0.3-11+b2
 Auto-Built-Package: debug-symbols
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 3416
 Depends: centrifuge (= 1.0.3-11+b2)
 Section: debug
 Priority: optional
 Description: debug symbols for centrifuge
 Build-Ids: 2530bc31c661c95dcd44ee303eda5ce6a191407e 37b63f1972a6ffa3b338b78485c3813749829c27 8eb43823ae1239c1d93a47f559edd75f722be0b1

drwxr-xr-x root/root         0 2024-01-19 18:06 ./
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/debug/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/debug/.build-id/25/
-rw-r--r-- root/root    797320 2024-01-19 18:06 ./usr/lib/debug/.build-id/25/30bc31c661c95dcd44ee303eda5ce6a191407e.debug
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/debug/.build-id/37/
-rw-r--r-- root/root    918036 2024-01-19 18:06 ./usr/lib/debug/.build-id/37/b63f1972a6ffa3b338b78485c3813749829c27.debug
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/debug/.build-id/8e/
-rw-r--r-- root/root   1532268 2024-01-19 18:06 ./usr/lib/debug/.build-id/8e/b43823ae1239c1d93a47f559edd75f722be0b1.debug
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root    234288 2024-01-19 18:06 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/centrifuge.debug
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/share/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/share/doc/
lrwxrwxrwx root/root         0 2024-01-19 18:06 ./usr/share/doc/centrifuge-dbgsym -> centrifuge


centrifuge_1.0.3-11+b2_armhf.deb
--------------------------------

 new Debian package, version 2.0.
 size 466812 bytes: control archive=1836 bytes.
    1203 bytes,    22 lines      control
    2338 bytes,    31 lines      md5sums
 Package: centrifuge
 Source: centrifuge (1.0.3-11)
 Version: 1.0.3-11+b2
 Architecture: armhf
 Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
 Installed-Size: 1406
 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.5), libstdc++6 (>= 13.1), 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 2024-01-19 18:06 ./
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/bin/
-rwxr-xr-x root/root       312 2022-10-10 05:52 ./usr/bin/centrifuge
lrwxrwxrwx root/root         0 2024-01-19 18:06 ./usr/bin/centrifuge-build -> centrifuge
lrwxrwxrwx root/root         0 2024-01-19 18:06 ./usr/bin/centrifuge-compress -> centrifuge
lrwxrwxrwx root/root         0 2024-01-19 18:06 ./usr/bin/centrifuge-download -> centrifuge
lrwxrwxrwx root/root         0 2024-01-19 18:06 ./usr/bin/centrifuge-inspect -> centrifuge
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/centrifuge/
-rwxr-xr-x root/root     19883 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge
-rwxr-xr-x root/root     12126 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-BuildSharedSequence.pl
-rwxr-xr-x root/root       407 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-RemoveEmptySequence.pl
-rwxr-xr-x root/root      1007 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-RemoveN.pl
-rwxr-xr-x root/root      2312 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-build
-rwxr-xr-x root/root    389756 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-build-bin
-rwxr-xr-x root/root    516840 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-class
-rwxr-xr-x root/root     13305 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-compress.pl
-rwxr-xr-x root/root     11670 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-download
-rwxr-xr-x root/root      1868 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-inspect
-rwxr-xr-x root/root    304900 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-inspect-bin
-rwxr-xr-x root/root      5231 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-kreport
-rwxr-xr-x root/root      3214 2024-01-19 18:06 ./usr/lib/centrifuge/centrifuge-sort-nt.pl
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/centrifuge/share/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/centrifuge/share/centrifuge/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/lib/centrifuge/share/centrifuge/indices/
-rw-r--r-- root/root     12887 2024-01-19 18:06 ./usr/lib/centrifuge/share/centrifuge/indices/Makefile
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/share/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/share/doc/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/share/doc/centrifuge/
-rw-r--r-- root/root       219 2024-01-19 18:06 ./usr/share/doc/centrifuge/changelog.Debian.armhf.gz
-rw-r--r-- root/root      1025 2024-01-19 18:06 ./usr/share/doc/centrifuge/changelog.Debian.gz
-rw-r--r-- root/root      1054 2022-10-10 05:52 ./usr/share/doc/centrifuge/copyright
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/
-rw-r--r-- root/root      1234 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/add.css
-rw-r--r-- root/root      1158 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/faq.shtml
-rw-r--r-- root/root       423 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/footer.inc.html
-rw-r--r-- root/root      2388 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/index.shtml.gz
-rw-r--r-- root/root     84288 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/manual.html
-rw-r--r-- root/root      1068 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/manual.shtml
-rw-r--r-- root/root      1348 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/sidebar.inc.shtml.gz
-rw-r--r-- root/root      7942 2024-01-19 18:06 ./usr/share/doc/centrifuge/html/style.css
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/share/man/
drwxr-xr-x root/root         0 2024-01-19 18:06 ./usr/share/man/man1/
-rw-r--r-- root/root      1204 2024-01-19 18:06 ./usr/share/man/man1/centrifuge-build.1.gz
-rw-r--r-- root/root       379 2024-01-19 18:06 ./usr/share/man/man1/centrifuge-compress.1.gz
-rw-r--r-- root/root       854 2024-01-19 18:06 ./usr/share/man/man1/centrifuge-download.1.gz
-rw-r--r-- root/root       920 2024-01-19 18:06 ./usr/share/man/man1/centrifuge-inspect.1.gz
-rw-r--r-- root/root      1931 2024-01-19 18:06 ./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: 32724
Build-Time: 176
Distribution: trixie-staging
Host Architecture: armhf
Install-Time: 518
Job: centrifuge_1.0.3-11
Machine Architecture: armhf
Package: centrifuge
Package-Time: 732
Source-Version: 1.0.3-11
Space: 32724
Status: successful
Version: 1.0.3-11+b2
--------------------------------------------------------------------------------
Finished at 2024-01-19T18:09:19Z
Build needed 00:12:12, 32724k disk space