centrifuge →
1.0.3-10+b2 →
armhf → 2022-02-13 00:53:30
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testbuildd
+==============================================================================+
| centrifuge 1.0.3-10+b2 (armhf) Sun, 13 Feb 2022 00:36:47 +0000 |
+==============================================================================+
Package: centrifuge
Version: 1.0.3-10+b2
Source Version: 1.0.3-10
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-caa0f937-e510-44f4-9aad-7ece97252544' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.8 MB]
Fetched 12.8 MB in 15s (835 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'centrifuge' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/centrifuge.git
Please use:
git clone https://salsa.debian.org/med-team/centrifuge.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 718 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main centrifuge 1.0.3-10 (dsc) [2037 B]
Get:2 http://172.17.4.1/private bookworm-staging/main centrifuge 1.0.3-10 (tar) [701 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main centrifuge 1.0.3-10 (diff) [14.7 kB]
Fetched 718 kB in 0s (2754 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/centrifuge-gc4jGB/centrifuge-1.0.3' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/centrifuge-gc4jGB' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-dY9lnN/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-dY9lnN/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-dY9lnN/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (2845 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core 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:
libperl5.32 netbase perl-modules-5.32 sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (22.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14442 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-python3, jellyfish
Filtered Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-python3, jellyfish
dpkg-deb: building package 'sbuild-build-depends-centrifuge-dummy' in '/<<BUILDDIR>>/resolver-dY9lnN/apt_archive/sbuild-build-depends-centrifuge-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-centrifuge-dummy sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ Sources [518 B]
Get:5 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ Packages [600 B]
Fetched 2451 B in 1s (3294 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install centrifuge 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:
libperl5.32 netbase perl-modules-5.32
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian jellyfish libarchive-zip-perl
libbrotli1 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu67
libjellyfish-2.0-2 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librtmp1 libsigsegv2 libssh2-1 libsub-override-perl
libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3
python3-distutils python3-lib2to3 python3-minimal python3.9
python3.9-minimal
Suggested packages:
autoconf-archive gnu-standards autoconf-doc dh-make flit python3-build
python3-tomli python3-installer gettext-doc libasprintf-dev libgettextpo-dev
groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser libmail-box-perl python3-doc python3-tk python3-venv
python3.9-venv python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl publicsuffix
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism dwz file gettext
gettext-base groff-base intltool-debian jellyfish libarchive-zip-perl
libbrotli1 libcurl3-gnutls libdebhelper-perl libdeflate0 libelf1 libexpat1
libfile-stripnondeterminism-perl libhts3 libhtscodecs2 libicu67
libjellyfish-2.0-2 libmagic-mgc libmagic1 libmpdec3 libnghttp2-14
libpipeline1 libpsl5 libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librtmp1 libsigsegv2 libssh2-1 libsub-override-perl
libtool libuchardet0 libxml2 m4 man-db media-types po-debconf python3
python3-distutils python3-lib2to3 python3-minimal python3.9
python3.9-minimal sbuild-build-depends-centrifuge-dummy
0 upgraded, 55 newly installed, 0 to remove and 0 not upgraded.
Need to get 24.7 MB of archives.
After this operation, 91.1 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-dY9lnN/apt_archive ./ sbuild-build-depends-centrifuge-dummy 0.invalid.0 [884 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.10-1+rpi1 [794 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.4-1 [82.4 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.10-1+rpi1 [1595 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.7-1+b4 [38.7 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf media-types all 5.0.0 [32.5 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.10-1+rpi1 [1611 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf python3.9 armhf 3.9.10-1+rpi1 [488 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.7-1+b4 [21.8 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.9.7-1+b4 [38.3 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.3-1 [136 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.5-1 [32.9 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.0-2 [1356 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.6 [193 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.6 [1054 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.10-1 [79.4 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.9.10-1 [146 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220119 [110 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-2 [161 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.81.0-1 [315 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.8-1 [44.1 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.1.1-3 [49.8 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.13+ds-2 [339 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libjellyfish-2.0-2 armhf 2.3.0-12 [56.4 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf jellyfish armhf 2.3.0-12 [621 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libsigsegv2:armhf (2.14-1) ...
Setting up autopoint (0.21-4) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.10.0-2) ...
Setting up libelf1:armhf (0.186-1) ...
Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libpython3.9-stdlib:armhf (3.9.10-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.7-1+b4) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-4) ...
Setting up libtool (2.4.6-15) ...
Setting up m4 (1.4.18-5) ...
Setting up libcurl3-gnutls:armhf (7.81.0-1) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up autoconf (2.71-2) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up groff-base (1.22.4-8) ...
Setting up python3.9 (3.9.10-1+rpi1) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libhts3:armhf (1.13+ds-2) ...
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Setting up python3 (3.9.7-1+b4) ...
Setting up man-db (2.10.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up dh-autoreconf (20) ...
Setting up jellyfish (2.3.0-12) ...
Setting up python3-lib2to3 (3.9.10-1) ...
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Setting up dh-python (5.20220119) ...
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Processing triggers for libc-bin (2.33-5+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37.90.20220130-2+rpi2 dpkg-dev_1.21.1+rpi1 g++-11_11.2.0-14+rpi1 gcc-11_11.2.0-14+rpi1 libc6-dev_2.33-5+rpi1 libstdc++-11-dev_11.2.0-14+rpi1 libstdc++6_11.2.0-14+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.15 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20220109.1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-6 binutils_2.37.90.20220130-2+rpi2 binutils-arm-linux-gnueabihf_2.37.90.20220130-2+rpi2 binutils-common_2.37.90.20220130-2+rpi2 bsdextrautils_2.37.3-1 bsdutils_1:2.37.3-1 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-14+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.6 debianutils_4.11.2 dh-autoreconf_20 dh-python_5.20220119 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3 dpkg_1.21.1+rpi1 dpkg-dev_1.21.1+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.27-1 file_1:5.41-2 findutils_4.8.0-1 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-14+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-14+rpi1 gcc-11-base_11.2.0-14+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3 gpg_2.2.27-3 gpg-agent_2.2.27-3 gpg-wks-client_2.2.27-3 gpg-wks-server_2.2.27-3 gpgconf_2.2.27-3 gpgsm_2.2.27-3 gpgv_2.2.27-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4 hostname_3.23 init-system-helpers_1.61 intltool-debian_0.35.0+20060710.5 jellyfish_2.3.0-12 libacl1_2.3.1-1 libapt-pkg6.0_2.3.15 libarchive-zip-perl_1.68-1 libasan6_11.2.0-14+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-14+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37.90.20220130-2+rpi2 libblkid1_2.37.3-1 libbrotli1_1.0.9-2+b1 libbz2-1.0_1.0.8-5 libc-bin_2.33-5+rpi1 libc-dev-bin_2.33-5+rpi1 libc6_2.33-5+rpi1 libc6-dev_2.33-5+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-14+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.37.90.20220130-2+rpi2 libctf0_2.37.90.20220130-2+rpi2 libcurl3-gnutls_7.81.0-1 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.6 libdeflate0_1.8-1 libdpkg-perl_1.21.1+rpi1 libelf1_0.186-1 libexpat1_2.4.4-1 libext2fs2_1.46.5-2 libfakeroot_1.27-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-11-dev_11.2.0-14+rpi1 libgcc-s1_11.2.0-14+rpi1 libgcrypt20_1.9.4-5 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.3-4 libgomp1_11.2.0-14+rpi1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libhts3_1.13+ds-2 libhtscodecs2_1.1.1-3 libicu67_67.1-7 libidn2-0_2.3.2-2 libisl23_0.24-2 libjellyfish-2.0-2_2.3.0-12 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmount1_2.37.3-1 libmpc3_1.2.1-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.3-2 libnettle8_3.7.3-1 libnghttp2-14_1.43.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libperl5.34_5.34.0-3 libpipeline1_1.5.5-1 libpsl5_0.21.0-1.2 libpython3-stdlib_3.9.7-1+b4 libpython3.9-minimal_3.9.10-1+rpi1 libpython3.9-stdlib_3.9.10-1+rpi1 libreadline8_8.1.2-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.27+dfsg2-3 libsasl2-modules-db_2.1.27+dfsg2-3 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.37.3-1 libsqlite3-0_3.37.2-2 libss2_1.46.5-2 libssh2-1_1.10.0-2 libssl1.1_1.1.1m-1 libstdc++-11-dev_11.2.0-14+rpi1 libstdc++6_11.2.0-14+rpi1 libsub-override-perl_0.09-2 libsystemd0_250.3-2+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-14+rpi1 libuchardet0_0.0.7-1 libudev1_250.3-2+rpi1 libunistring2_1.0-1 libuuid1_2.37.3-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.11.1+dfsg1-1 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.0-2 mawk_1.3.4.20200120-3 media-types_5.0.0 mount_2.37.3-1 ncurses-base_6.3-2 ncurses-bin_6.3-2 netbase_6.3 passwd_1:4.11.1+dfsg1-1 patch_2.7.6-7 perl_5.34.0-3 perl-base_5.34.0-3 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-3 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 python3_3.9.7-1+b4 python3-distutils_3.9.10-1 python3-lib2to3_3.9.10-1 python3-minimal_3.9.7-1+b4 python3.9_3.9.10-1+rpi1 python3.9-minimal_3.9.10-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-centrifuge-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.01-1 tar_1.34+dfsg-1 tzdata_2021e-1 util-linux_2.37.3-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.yMSkgTBu/trustedkeys.kbx': General error
gpgv: Signature made Sun Dec 5 20:20:35 2021 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./centrifuge_1.0.3-10.dsc
dpkg-source: info: extracting centrifuge in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking centrifuge_1.0.3.orig.tar.gz
dpkg-source: info: unpacking centrifuge_1.0.3-10.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying fix_auto_ptr_usage_in_gcc-7.patch
dpkg-source: info: applying 0002-Fix-build-with-rank.patch
dpkg-source: info: applying 0003-Fix-make-install-DESTDIR.patch
dpkg-source: info: applying hardening.patch
dpkg-source: info: applying no_msse2.patch
dpkg-source: info: applying 2to3.patch
dpkg-source: info: applying fix_arm_build.patch
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.0.3-10+b2
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-caa0f937-e510-44f4-9aad-7ece97252544
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package centrifuge
dpkg-buildpackage: info: source version 1.0.3-10+b2
dpkg-buildpackage: info: source distribution bookworm-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="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DBOWTIE_MM -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
\
-o centrifuge-build-bin centrifuge_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp centrifuge_build_main.cpp \
-lpthread
/usr/bin/g++ -O3 -funroll-loops -g3 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 \"" \
-fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DBOWTIE_MM -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
\
-o centrifuge-class centrifuge.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp ref_coord.cpp mask.cpp pe.cpp aligner_seed_policy.cpp scoring.cpp presets.cpp simple_func.cpp random_util.cpp outq.cpp centrifuge_main.cpp \
-lpthread
/usr/bin/g++ -O3 -funroll-loops -g3 \
-DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 \"" \
-fno-strict-aliasing -DCENTRIFUGE_VERSION="\"1.0.3-beta\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DBOWTIE_MM -Wl,-z,relro -Wl,-z,now -DCENTRIFUGE -DBOWTIE2 -DBOWTIE_64BIT_INDEX -Wall \
-I . \
-o centrifuge-inspect-bin centrifuge_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp bt2_idx.cpp reference.cpp ds.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread
In file included from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:175:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:176:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_idx.h:44,
from centrifuge_build.cpp:27:
blockwise_sa.h: In function 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
490 | mkeyQSortSuf(t, s, slen, 4,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
491 | this->verbose(), this->sanityCheck());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
In file included from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge.cpp:34:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:175:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:176:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_idx.h:44,
from centrifuge.cpp:34:
blockwise_sa.h: In function 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
490 | mkeyQSortSuf(t, s, slen, 4,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
491 | this->verbose(), this->sanityCheck());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro 'OFF_MASK'
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ^~~~~~~~
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:15: required from here
multikey_qsort.h:496:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro 'OFF_MASK'
1155 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro 'OFF_MASK'
1164 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
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);
| ^~~~~~~~
In file included from centrifuge_build.cpp:27:
bt2_idx.h: In instantiation of 'void Ebwt<index_t>::buildToDisk(InorderBlockwiseSA<TStr>&, const TStr&, std::ostream&, std::ostream&, std::ostream*, std::ostream*, const EList<RefRecord>&, int) [with TStr = SString<char>; index_t = long long unsigned int; std::ostream = std::basic_ostream<char>]':
bt2_idx.h:1492:16: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
bt2_idx.h:3452:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
3452 | for(size_t k = 0; k < kmer_size; k++) {
| ~~^~~~~~~~~~~
bt2_idx.h:3641:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
3641 | for(size_t k = 0; k < kmer_size; k++) {
| ~~^~~~~~~~~~~
bt2_idx.h: In instantiation of 'void Ebwt<index_t>::buildToDisk(InorderBlockwiseSA<TStr>&, const TStr&, std::ostream&, std::ostream&, std::ostream*, std::ostream*, const EList<RefRecord>&, int) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ostream = std::basic_ostream<char>]':
bt2_idx.h:1492:16: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:697:25: required from here
bt2_idx.h:3452:41: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
3452 | for(size_t k = 0; k < kmer_size; k++) {
| ~~^~~~~~~~~~~
bt2_idx.h:3641:27: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'unsigned int'} and 'int' [-Wsign-compare]
3641 | for(size_t k = 0; k < kmer_size; k++) {
| ~~^~~~~~~~~~~
In file included from bt2_idx.h:44,
from hier_idx.h:24,
from centrifuge_inspect.cpp:28:
blockwise_sa.h: In function 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
490 | mkeyQSortSuf(t, s, slen, 4,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
491 | this->verbose(), this->sanityCheck());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
In file included from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
diff_sample.h: In instantiation of 'void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]':
blockwise_sa.h:383:20: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
diff_sample.h:813:43: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
813 | sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff_sample.h:813:43: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
diff_sample.h: In instantiation of 'void DifferenceCoverSample<T>::build(int) [with TStr = S2bDnaString]':
blockwise_sa.h:383:20: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:697:25: required from here
diff_sample.h:813:43: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
diff_sample.h:813:43: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList<unsigned int>*) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]':
diff_sample.h:772:30: required from 'void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]'
blockwise_sa.h:383:20: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
multikey_qsort.h:661:39: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
661 | sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from bt2_idx.h:44,
from centrifuge_build.cpp:27:
blockwise_sa.h: In instantiation of 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]':
blockwise_sa.h:607:9: required from 'void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]'
blockwise_sa.h:388:4: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
blockwise_sa.h:460:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
460 | mkeyQSortSuf(t, s, slen, 4,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
461 | this->verbose(), this->sanityCheck());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h:460:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList<unsigned int>*) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
diff_sample.h:772:30: required from 'void DifferenceCoverSample<T>::build(int) [with TStr = S2bDnaString]'
blockwise_sa.h:383:20: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = S2bDnaString]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = S2bDnaString]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = S2bDnaString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = S2bDnaString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = S2bDnaString; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:697:25: required from here
multikey_qsort.h:661:39: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
661 | sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]':
blockwise_sa.h:454:19: required from 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]'
blockwise_sa.h:607:9: required from 'void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]'
blockwise_sa.h:388:4: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro 'OFF_MASK'
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ^~~~~~~~
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:460:15: required from 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]'
blockwise_sa.h:607:9: required from 'void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]'
blockwise_sa.h:388:4: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
multikey_qsort.h:496:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge_build.cpp:27:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]':
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:454:19: required from 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]'
blockwise_sa.h:607:9: required from 'void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]'
blockwise_sa.h:388:4: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro 'OFF_MASK'
1155 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro 'OFF_MASK'
1164 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:454:19: required from 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]'
blockwise_sa.h:607:9: required from 'void KarkkainenBlockwiseSA<TStr>::buildSamples() [with TStr = SString<char>]'
blockwise_sa.h:388:4: required from 'void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]'
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro 'OFF_MASK'
1066 | OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1062:33: required from 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]'
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:454:19: required from 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]'
blockwise_sa.h:607:9: [ skipping 2 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
blockwise_sa.h:362:4: required from 'void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]'
blockwise_sa.h:215:29: required from 'KarkkainenBlockwiseSA<TStr>::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ostream = std::basic_ostream<char>]'
bt2_idx.h:1488:33: required from 'void Ebwt<index_t>::initFromVector(TStr&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, std::ofstream*, std::ofstream*, int, const string&, const string&, const string&, const string&, const string&, bool, index_t, index_t, index_t, int, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::ofstream = std::basic_ofstream<char>; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
bt2_idx.h:881:23: required from 'Ebwt<index_t>::Ebwt(TStr&, bool, int, int, int32_t, int32_t, int32_t, const string&, bool, bool, index_t, index_t, index_t, int, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const string&, const string&, const string&, const string&, const RefReadInParams&, uint32_t, int32_t, bool, bool, int, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]'
centrifuge_build.cpp:472:19: required from 'void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]'
centrifuge_build.cpp:677:28: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro 'OFF_MASK'
914 | off = OFF_MASK;
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro 'OFF_MASK'
923 | OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro 'OFF_MASK'
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge.cpp:34:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro 'OFF_MASK'
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ^~~~~~~~
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge.cpp:34:
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:15: required from here
multikey_qsort.h:496:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from centrifuge.cpp:47:
classifier.h: In instantiation of 'int Classifier<index_t, local_index_t>::go(const Scoring&, const Ebwt<index_t>&, const Ebwt<index_t>&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, SpeciesMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]':
centrifuge.cpp:2660:34: required from here
classifier.h:411:30: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
411 | if(i + 1 < _hitMap.size()) {
| ~~~~~~^~~~~~~~~~~~~~~~
classifier.h:432:48: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
432 | if(_hitMap[i].rank + 1 >= _hitMap[i].path.size()) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
classifier.h:442:55: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
442 | uint64_t parent_taxID = (rank + 1 >= _hitMap[i].path.size() ? 1 : _hitMap[i].path[rank + 1]);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
classifier.h:475:63: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
475 | uint64_t cur_parent_taxID = (rank + 1 >= _hitMap[i].path.size() ? 1 : _hitMap[i].path[rank + 1]);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge.cpp:34:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro 'OFF_MASK'
1155 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro 'OFF_MASK'
1164 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from centrifuge.cpp:47:
classifier.h: In instantiation of 'void Classifier<index_t, local_index_t>::searchForwardAndReverse(index_t, const Ebwt<index_t>&, const Scoring&, RandomSource&, const ReportingParams&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]':
classifier.h:238:13: required from 'int Classifier<index_t, local_index_t>::go(const Scoring&, const Ebwt<index_t>&, const Ebwt<index_t>&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, SpeciesMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]'
centrifuge.cpp:2660:34: required from here
classifier.h:850:50: warning: comparison of integer expressions of different signedness: 'long long unsigned int' and 'const THitInt' {aka 'const long long int'} [-Wsign-compare]
850 | hit.size() + rchit.size() > rp.ihits) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
classifier.h:647:16: warning: variable 'cur' set but not used [-Wunused-but-set-variable]
647 | size_t cur[2] = {0, 0} ;
| ^~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from centrifuge.cpp:34:
multikey_qsort.h: In instantiation of 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro 'OFF_MASK'
1066 | OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1062:33: required from 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]'
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro 'OFF_MASK'
914 | off = OFF_MASK;
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro 'OFF_MASK'
923 | OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro 'OFF_MASK'
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from centrifuge.cpp:41:
aln_sink.h: In instantiation of 'void AlnSinkSam<index_t>::appendMate(Ebwt<index_t>&, BTString&, const Read&, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable<char, 1024, 2>; TReadId = long long unsigned int; size_t = unsigned int]':
aln_sink.h:1407:9: required from 'void AlnSinkSam<index_t>::append(BTString&, size_t, const Read*, const Read*, TReadId, AlnRes*, AlnRes*, const AlnSetSumm&, const PerReadMetrics&, SpeciesMetrics&, bool, size_t) [with index_t = long long unsigned int; BTString = SStringExpandable<char, 1024, 2>; size_t = unsigned int; TReadId = long long unsigned int]'
aln_sink.h:1392:15: required from here
aln_sink.h:2302:25: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'unsigned int'} [-Wsign-compare]
2302 | for (int i=0; i < this->tab_fmt_cols_.size(); ++i) {
| ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from hier_idx.h:24,
from centrifuge_inspect.cpp:28:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro 'OFF_MASK'
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ^~~~~~~~
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from hier_idx.h:24,
from centrifuge_inspect.cpp:28:
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:15: required from here
multikey_qsort.h:496:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from hier_idx.h:24,
from centrifuge_inspect.cpp:28:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro 'OFF_MASK'
1155 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro 'OFF_MASK'
1164 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro 'OFF_MASK'
1066 | OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1062:33: required from 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]'
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro 'OFF_MASK'
914 | off = OFF_MASK;
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro 'OFF_MASK'
923 | OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro 'OFF_MASK'
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from /usr/include/c++/11/set:60,
from centrifuge_inspect.cpp:24:
/usr/include/c++/11/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const long long unsigned int&>, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair<const long long unsigned int, long long unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, long long unsigned int> >]':
/usr/include/c++/11/bits/stl_tree.h:2428:7: 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
2428 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/map:61,
from bt2_idx.h:34,
from hier_idx.h:24,
from centrifuge_inspect.cpp:28:
/usr/include/c++/11/bits/stl_map.h: In constructor 'Ebwt<index_t>::Ebwt(const string&, int, int, bool, int32_t, int32_t, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool, bool) [with index_t = long long unsigned int]':
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_map.h:501:44: note: parameter passing for argument of type 'std::_Rb_tree<long long unsigned int, std::pair<const long long unsigned int, long long unsigned int>, std::_Select1st<std::pair<const long long unsigned int, long long unsigned int> >, std::less<long long unsigned int>, std::allocator<std::pair<const long long unsigned int, long long unsigned int> > >::const_iterator' changed in GCC 7.1
501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
502 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
503 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:175:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:176:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_idx.h:44,
from bt2_idx.cpp:25:
blockwise_sa.h: In function 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
490 | mkeyQSortSuf(t, s, slen, 4,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
491 | this->verbose(), this->sanityCheck());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro 'OFF_MASK'
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ^~~~~~~~
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:15: required from here
multikey_qsort.h:496:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro 'OFF_MASK'
1155 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro 'OFF_MASK'
1164 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro 'OFF_MASK'
1066 | OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1062:33: required from 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]'
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro 'OFF_MASK'
914 | off = OFF_MASK;
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro 'OFF_MASK'
923 | OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro 'OFF_MASK'
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:175:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:176:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_idx.h:44,
from bt2_idx.cpp:25:
blockwise_sa.h: In function 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
490 | mkeyQSortSuf(t, s, slen, 4,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
491 | this->verbose(), this->sanityCheck());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro 'OFF_MASK'
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ^~~~~~~~
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:15: required from here
multikey_qsort.h:496:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro 'OFF_MASK'
1155 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro 'OFF_MASK'
1164 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro 'OFF_MASK'
1066 | OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1062:33: required from 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]'
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro 'OFF_MASK'
914 | off = OFF_MASK;
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro 'OFF_MASK'
923 | OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro 'OFF_MASK'
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:175:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:176:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
In file included from bt2_idx.h:44,
from bt2_idx.cpp:25:
blockwise_sa.h: In function 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
490 | mkeyQSortSuf(t, s, slen, 4,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
491 | this->verbose(), this->sanityCheck());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = S2bDnaString]':
blockwise_sa.h:490:29: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:70: note: in expansion of macro 'OFF_MASK'
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ^~~~~~~~
In file included from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h:764:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
multikey_qsort.h: In instantiation of 'void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]':
blockwise_sa.h:490:15: required from here
multikey_qsort.h:496:47: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from multikey_qsort.h:24,
from diff_sample.h:26,
from blockwise_sa.h:29,
from bt2_idx.h:44,
from bt2_idx.cpp:25:
multikey_qsort.h: In instantiation of 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]':
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1155:70: note: in expansion of macro 'OFF_MASK'
1155 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1164:70: note: in expansion of macro 'OFF_MASK'
1164 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1066:40: note: in expansion of macro 'OFF_MASK'
1066 | OFF_MASK, begin, end);
| ^~~~~~~~
multikey_qsort.h: In instantiation of 'void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]':
multikey_qsort.h:1062:33: required from 'void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]'
multikey_qsort.h:1161:20: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
multikey_qsort.h:763:18: required from 'void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]'
blockwise_sa.h:484:19: required from here
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:914:31: note: in expansion of macro 'OFF_MASK'
914 | off = OFF_MASK;
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:923:64: note: in expansion of macro 'OFF_MASK'
923 | OFF_MASK, begin, end);
| ^~~~~~~~
btypes.h:25:18: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow]
25 | #define OFF_MASK 0xffffffffffffffff
| ^~~~~~~~~~~~~~~~~~
multikey_qsort.h:1007:62: note: in expansion of macro 'OFF_MASK'
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from diff_sample.cpp:20:
diff_sample.h: In function 'void calcExhaustiveDC(T, bool, bool)':
diff_sample.h:175:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~
diff_sample.h:175:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
175 | if(!diffs[d1]) diffCnt++; diffs[d1] = true;
| ^~~~~
diff_sample.h:176:41: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~
diff_sample.h:176:67: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
176 | if(!diffs[d2]) diffCnt++; diffs[d2] = true;
| ^~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
dh_prep -a
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install -- prefix=/usr/lib/centrifuge
make -j4 install DESTDIR=/<<PKGBUILDDIR>>/debian/centrifuge AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" prefix=/usr/lib/centrifuge
make[2]: Entering directory '/<<PKGBUILDDIR>>'
mkdir -p /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/bin
mkdir -p /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/indices
install -m 0644 indices/Makefile /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/indices
install -d -m 0755 /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc
install -m 0644 doc/* /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc
for file in centrifuge-build-bin centrifuge-class centrifuge-inspect-bin centrifuge centrifuge-build centrifuge-inspect centrifuge-download centrifuge-kreport centrifuge-BuildSharedSequence.pl centrifuge-RemoveEmptySequence.pl centrifuge-RemoveN.pl centrifuge-compress.pl centrifuge-sort-nt.pl; do \
install -m 0755 $file /<<PKGBUILDDIR>>/debian/centrifuge/usr/lib/centrifuge/bin ; \
done
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
mv debian/centrifuge/usr/lib/centrifuge/bin/* debian/centrifuge/usr/lib/centrifuge/
rmdir debian/centrifuge/usr/lib/centrifuge/bin
# move documentation to correct location
mkdir -p debian/centrifuge/usr/share/doc/centrifuge/html
mv debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc/*html \
debian/centrifuge/usr/lib/centrifuge/share/centrifuge/doc/*css \
debian/centrifuge/usr/share/doc/centrifuge/html
# remove useless stuff in documentation dir
rm -rf debian/centrifuge/usr/lib/centrifuge/share/doc/
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
rm -rf debian/*/usr/lib/centrifuge/share/centrifuge/doc
find debian -name manual.inc.html | xargs rm -rf
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_python3 -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
dh_fixperms -a
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dpkg-shlibdeps: warning: debian/centrifuge/usr/lib/centrifuge/centrifuge-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-class contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/centrifuge/usr/lib/centrifuge/centrifuge-build-bin contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/centrifuge/usr/lib/centrifuge/centrifuge-inspect-bin debian/centrifuge/usr/lib/centrifuge/centrifuge-class 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_1.0.3-10+b2_armhf.deb'.
dpkg-deb: building package 'centrifuge-dbgsym' in '../centrifuge-dbgsym_1.0.3-10+b2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../centrifuge_1.0.3-10+b2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../centrifuge_1.0.3-10+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 2022-02-13T00:53:21Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
centrifuge_1.0.3-10+b2_armhf.changes:
-------------------------------------
Format: 1.8
Date: Sun, 05 Dec 2021 21:16:55 +0100
Source: centrifuge (1.0.3-10)
Binary: centrifuge centrifuge-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.0.3-10+b2
Distribution: bookworm-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
centrifuge - rapid and memory-efficient system for classification of DNA seque
Changes:
centrifuge (1.0.3-10+b2) bookworm-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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2a7cd2f7bd12ca2250ec677d05a357ce02b34a7f 6419 centrifuge_1.0.3-10+b2_armhf.buildinfo
91e0dfb0b0a2becfea9a917c9fbfca56d5f17e1a 464572 centrifuge_1.0.3-10+b2_armhf.deb
Checksums-Sha256:
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de9c61517b0a27512c0f178447acfaa996768565ad00344d160698a78d70102a 6419 centrifuge_1.0.3-10+b2_armhf.buildinfo
47318b7eb35c0810c91c84962188948ad2fc13fbf03b659986e98fb743ae4d12 464572 centrifuge_1.0.3-10+b2_armhf.deb
Files:
480a9ef1bb6e5c779bc6511819beff16 3401928 debug optional centrifuge-dbgsym_1.0.3-10+b2_armhf.deb
dbadf879964ff3eb7a8946ca6b528c2f 6419 science optional centrifuge_1.0.3-10+b2_armhf.buildinfo
412bb460af340bf4360e69def55e8dca 464572 science optional centrifuge_1.0.3-10+b2_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
centrifuge-dbgsym_1.0.3-10+b2_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 3401928 bytes: control archive=704 bytes.
484 bytes, 12 lines control
408 bytes, 4 lines md5sums
Package: centrifuge-dbgsym
Source: centrifuge (1.0.3-10)
Version: 1.0.3-10+b2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3483
Depends: centrifuge (= 1.0.3-10+b2)
Section: debug
Priority: optional
Description: debug symbols for centrifuge
Build-Ids: 1df73bc17ca1a55690a896edd6a8ee80edb96a59 34491523121f59de3788016b36878a0fd196b62d 9c0ca39d62b3d1de32ab4a37c68f5d6360db95f3
drwxr-xr-x root/root 0 2021-12-05 20:16 ./
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/debug/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/debug/.build-id/1d/
-rw-r--r-- root/root 797376 2021-12-05 20:16 ./usr/lib/debug/.build-id/1d/f73bc17ca1a55690a896edd6a8ee80edb96a59.debug
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/debug/.build-id/34/
-rw-r--r-- root/root 960216 2021-12-05 20:16 ./usr/lib/debug/.build-id/34/491523121f59de3788016b36878a0fd196b62d.debug
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/debug/.build-id/9c/
-rw-r--r-- root/root 1546020 2021-12-05 20:16 ./usr/lib/debug/.build-id/9c/0ca39d62b3d1de32ab4a37c68f5d6360db95f3.debug
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 246844 2021-12-05 20:16 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/centrifuge.debug
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/share/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/share/doc/
lrwxrwxrwx root/root 0 2021-12-05 20:16 ./usr/share/doc/centrifuge-dbgsym -> centrifuge
centrifuge_1.0.3-10+b2_armhf.deb
--------------------------------
new Debian package, version 2.0.
size 464572 bytes: control archive=1832 bytes.
1201 bytes, 22 lines control
2338 bytes, 31 lines md5sums
Package: centrifuge
Source: centrifuge (1.0.3-10)
Version: 1.0.3-10+b2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1378
Depends: libc6 (>= 2.33), libgcc-s1 (>= 3.5), libstdc++6 (>= 11), python3:any, python3, hisat2, jellyfish
Section: science
Priority: optional
Homepage: https://ccb.jhu.edu/software/centrifuge/
Description: rapid and memory-efficient system for classification of DNA sequences
Centrifuge is a very rapid and memory-efficient system for the
classification of DNA sequences from microbial samples, with better
sensitivity than and comparable accuracy to other leading systems. The
system uses a novel indexing scheme based on the Burrows-Wheeler
transform (BWT) and the Ferragina-Manzini (FM) index, optimized
specifically for the metagenomic classification problem. Centrifuge
requires a relatively small index (e.g., 4.3 GB for ~4,100 bacterial
genomes) yet provides very fast classification speed, allowing it to
process a typical DNA sequencing run within an hour. Together these
advances enable timely and accurate analysis of large metagenomics data
sets on conventional desktop computers.
drwxr-xr-x root/root 0 2021-12-05 20:16 ./
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/bin/
-rwxr-xr-x root/root 312 2021-12-05 20:16 ./usr/bin/centrifuge
lrwxrwxrwx root/root 0 2021-12-05 20:16 ./usr/bin/centrifuge-build -> centrifuge
lrwxrwxrwx root/root 0 2021-12-05 20:16 ./usr/bin/centrifuge-compress -> centrifuge
lrwxrwxrwx root/root 0 2021-12-05 20:16 ./usr/bin/centrifuge-download -> centrifuge
lrwxrwxrwx root/root 0 2021-12-05 20:16 ./usr/bin/centrifuge-inspect -> centrifuge
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/centrifuge/
-rwxr-xr-x root/root 19883 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge
-rwxr-xr-x root/root 12126 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-BuildSharedSequence.pl
-rwxr-xr-x root/root 407 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-RemoveEmptySequence.pl
-rwxr-xr-x root/root 1007 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-RemoveN.pl
-rwxr-xr-x root/root 2312 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-build
-rwxr-xr-x root/root 381564 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-build-bin
-rwxr-xr-x root/root 508648 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-class
-rwxr-xr-x root/root 13305 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-compress.pl
-rwxr-xr-x root/root 11670 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-download
-rwxr-xr-x root/root 1868 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-inspect
-rwxr-xr-x root/root 292612 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-inspect-bin
-rwxr-xr-x root/root 5231 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-kreport
-rwxr-xr-x root/root 3214 2021-12-05 20:16 ./usr/lib/centrifuge/centrifuge-sort-nt.pl
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/centrifuge/share/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/centrifuge/share/centrifuge/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/lib/centrifuge/share/centrifuge/indices/
-rw-r--r-- root/root 12887 2021-12-05 20:16 ./usr/lib/centrifuge/share/centrifuge/indices/Makefile
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/share/
drwxr-xr-x root/root 0 2021-12-05 20:16 ./usr/share/doc/
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 32952
Build-Time: 526
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 427
Job: centrifuge_1.0.3-10
Machine Architecture: armhf
Package: centrifuge
Package-Time: 994
Source-Version: 1.0.3-10
Space: 32952
Status: successful
Version: 1.0.3-10+b2
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Finished at 2022-02-13T00:53:21Z
Build needed 00:16:34, 32952k disc space