hisat2 →
2.1.0-2nopython3hisat3 →
armhf → 2020-01-07 16:08:02
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-02
+==============================================================================+
| hisat2 2.1.0-2nopython3hisat3 (armhf) Tue, 07 Jan 2020 15:57:13 +0000 |
+==============================================================================+
Package: hisat2
Version: 2.1.0-2nopython3hisat3
Source Version: 2.1.0-2nopython3hisat3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-afd0ffcf-3302-4f66-9a9a-21bc0b5d3909' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.7 MB]
Fetched 24.3 MB in 16s (1521 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: 'hisat2' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/hisat2.git
Please use:
git clone https://salsa.debian.org/med-team/hisat2.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 2827 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main hisat2 2.1.0-2nopython3hisat3 (dsc) [2069 B]
Get:2 http://172.17.0.1/private bullseye-staging/main hisat2 2.1.0-2nopython3hisat3 (tar) [2742 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main hisat2 2.1.0-2nopython3hisat3 (diff) [82.8 kB]
Fetched 2827 kB in 1s (4028 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hisat2-gEKfAe/hisat2-2.1.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hisat2-gEKfAe' 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-io2u5n/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-io2u5n/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-io2u5n/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: 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 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: 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-io2u5n/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (9989 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:
libpam-cap netbase
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 33 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
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Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 13002 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 (= 12), help2man, pandoc, python3
Filtered Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3
dpkg-deb: building package 'sbuild-build-depends-hisat2-dummy' in '/<<BUILDDIR>>/resolver-io2u5n/apt_archive/sbuild-build-depends-hisat2-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-hisat2-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-io2u5n/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ Sources [507 B]
Get:5 copy:/<<BUILDDIR>>/resolver-io2u5n/apt_archive ./ Packages [589 B]
Fetched 2429 B in 0s (11.5 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install hisat2 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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1
libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib libsigsegv2 libssl1.1 libsub-override-perl libtinfo5
libtool libuchardet0 libxml2 m4 man-db mime-support pandoc pandoc-data
po-debconf python3 python3-minimal python3.7 python3.7-minimal
sensible-utils
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less
www-browser texlive-latex-recommended texlive-xetex texlive-luatex
pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc
nodejs php python ruby r-base-core libjs-mathjax node-katex libmail-box-perl
python3-doc python3-tk python3-venv python3.7-venv python3.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base
groff-base help2man intltool-debian libarchive-zip-perl libbsd0 libcroco3
libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl
libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1
libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib libsigsegv2 libssl1.1 libsub-override-perl libtinfo5
libtool libuchardet0 libxml2 m4 man-db mime-support pandoc pandoc-data
po-debconf python3 python3-minimal python3.7 python3.7-minimal
sbuild-build-depends-hisat2-dummy sensible-utils
0 upgraded, 51 newly installed, 0 to remove and 33 not upgraded.
Need to get 43.5 MB of archives.
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Get:2 http://172.17.0.1/private bullseye-staging/main armhf liblocale-gettext-perl armhf 1.07-4 [18.1 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-1 [29.5 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1 [585 kB]
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Get:15 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.6-1 [1669 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1 [350 kB]
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Get:20 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.37-6 [253 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.37-6 [111 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.37-6 [66.2 kB]
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Get:27 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
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Get:33 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
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Get:37 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1 [1138 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.3 [1019 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.11 [180 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf pandoc-data all 2.5-3 [349 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf pandoc armhf 2.5-3 [18.6 MB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking sbuild-build-depends-hisat2-dummy (0.invalid.0) ...
Setting up libpipeline1:armhf (1.5.2-1) ...
Setting up mime-support (3.64) ...
Setting up libmagic-mgc (1:5.37-6) ...
Setting up libarchive-zip-perl (1.67-1) ...
Setting up libglib2.0-0:armhf (2.62.4-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (12.7.3) ...
Setting up libmagic1:armhf (1:5.37-6) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.37-6) ...
Setting up libicu63:armhf (63.2-2) ...
Setting up autotools-dev (20180224.1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up pandoc-data (2.5-3) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up liblocale-gettext-perl (1.07-4) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up libpython3.7-stdlib:armhf (3.7.6-1) ...
Setting up libtool (2.4.6-11) ...
Setting up m4 (1.4.18-4) ...
Setting up help2man (1.47.11) ...
Setting up pandoc (2.5-3) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up autoconf (2.69-11) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up libpython3-stdlib:armhf (3.7.5-3) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.6-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up python3 (3.7.5-3) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up po-debconf (1.0.21) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (12.7.3) ...
Setting up sbuild-build-depends-hisat2-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.29-3+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-58-generic armhf (armv8l)
Toolchain package versions: binutils_2.33.1-5+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-19+rpi1+b1 gcc-9_9.2.1-19+rpi1+b1 libc6-dev_2.29-3+rpi1 libstdc++-9-dev_9.2.1-19+rpi1+b1 libstdc++6_9.2.1-19+rpi1+b1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.46 bash_5.0-5 binutils_2.33.1-5+rpi1 binutils-arm-linux-gnueabihf_2.33.1-5+rpi1 binutils-common_2.33.1-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-19+rpi1+b1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.17-3+b1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.4-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.37-6 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-19+rpi1+b1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-19+rpi1+b1 gcc-9-base_9.2.1-19+rpi1+b1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.17-3 gnupg-l10n_2.2.17-3 gnupg-utils_2.2.17-3+b1 gpg_2.2.17-3+b1 gpg-agent_2.2.17-3+b1 gpg-wks-client_2.2.17-3+b1 gpg-wks-server_2.2.17-3+b1 gpgconf_2.2.17-3+b1 gpgsm_2.2.17-3+b1 gpgv_2.2.17-3+b1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 help2man_1.47.11 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-19+rpi1+b1 libassuan0_2.5.3-7 libatomic1_9.2.1-19+rpi1+b1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-5+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-3+rpi1 libc-dev-bin_2.29-3+rpi1 libc6_2.29-3+rpi1 libc6-dev_2.29-3+rpi1 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-19+rpi1+b1 libcom-err2_1.45.4-1 libcroco3_0.6.13-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.4-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libgcc-9-dev_9.2.1-19+rpi1+b1 libgcc1_1:9.2.1-19+rpi1+b1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.10-5 libgomp1_9.2.1-19+rpi1+b1 libgpg-error0_1.36-7 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.37-6 libmagic1_1:5.37-6 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-3 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-1 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libreadline7_7.0-5 libreadline8_8.0-3 librust-bitflags-dev_1.2.1-1 librust-cloudabi+default-dev_0.0.3-1 librust-cloudabi-dev_0.0.3-1 librust-fuchsia-zircon-dev_0.3.3-2 librust-fuchsia-zircon-sys-dev_0.3.3-2 librust-libc-dev_0.2.62-1 librust-phf-codegen-dev_0.7.23-1 librust-phf-generator-dev_0.7.23-1 librust-phf-shared-dev_0.7.23-2+b1 librust-rand-0.5+alloc-dev_0.5.5-2+rpi1 librust-rand-0.5+std-dev_0.5.5-2+rpi1 librust-rand-0.5-dev_0.5.5-2+rpi1 librust-rand-core-0.2+alloc-dev_0.2.2-1 librust-rand-core-0.2+std-dev_0.2.2-1 librust-rand-core-0.2-dev_0.2.2-1 librust-rand-core-dev_0.3.0-1 librust-siphasher-dev_0.2.3-1 librust-winapi-dev_0.3.6-1 librust-winapi-i686-pc-windows-gnu-dev_0.4.0-1 librust-winapi-x86-64-pc-windows-gnu-dev_0.4.0-1 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.4.2-2+rpi1 libselinux1_2.9-3 libsemanage-common_2.9-3 libsemanage1_2.9-3 libsepol1_2.9-2 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1-1 libss2_1.45.4-1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-19+rpi1+b1 libstdc++6_9.2.1-19+rpi1+b1 libsub-override-perl_0.09-2 libsystemd0_243-8+rpi1 libtasn1-6_4.14-3 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-19+rpi1+b1 libuchardet0_0.0.6-3 libudev1_243-8+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.4+dfsg1-8 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.7-2 logsave_1.45.4-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_5.7 pandoc_2.5-3 pandoc-data_2.5-3 passwd_1:4.7-2 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python3_3.7.5-3 python3-minimal_3.7.5-3 python3.7_3.7.6-1 python3.7-minimal_3.7.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-hisat2-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Sat Jan 4 21:52:32 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./hisat2_2.1.0-2nopython3hisat3.dsc
dpkg-source: info: extracting hisat2 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking hisat2_2.1.0.orig.tar.xz
dpkg-source: info: unpacking hisat2_2.1.0-2nopython3hisat3.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying hardening
dpkg-source: info: applying reproducibile
dpkg-source: info: applying fix-freebsd
dpkg-source: info: applying compilerflags
dpkg-source: info: applying simde
dpkg-source: info: applying python3
Check disk space
----------------
Sufficient free space for build
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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-afd0ffcf-3302-4f66-9a9a-21bc0b5d3909
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package hisat2
dpkg-buildpackage: info: source version 2.1.0-2nopython3hisat3
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug \
hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe \
hisat2-src.zip hisat2-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules build-arch
dh build-arch
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 -- BUILD_HOST='Debian' BUILD_TIME="04 January 2020" all doc
make -j4 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=04 January 2020" all doc
make[2]: Entering directory '/<<PKGBUILDDIR>>'
/usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"04 January 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
-I third_party \
-o hisat2-build-s hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread -Wl,-z,relro -Wl,-z,now
/usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"04 January 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I third_party \
-o hisat2-build-l hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread -Wl,-z,relro -Wl,-z,now
/usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"04 January 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \
-I third_party \
-o hisat2-align-s hisat2.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \
-lpthread -Wl,-z,relro -Wl,-z,now
/usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"04 January 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I third_party \
-o hisat2-align-l hisat2.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \
-lpthread -Wl,-z,relro -Wl,-z,now
In file included from gfm.h:43,
from hisat2_build.cpp:35:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from gfm.h:43,
from hgfm.h:24,
from hisat2.cpp:33:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from hisat2_build.cpp:35:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from hisat2_build.cpp:35:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from hisat2_build.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from hisat2_build.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from hisat2_build.cpp:35:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from hisat2_build.cpp:35:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from hisat2_build.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from hisat2_build.cpp:30:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from hgfm.h:24,
from hisat2.cpp:33:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from hgfm.h:24,
from hisat2.cpp:33:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from hgfm.h:24,
from hisat2.cpp:33:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from hgfm.h:24,
from hisat2.cpp:33:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from sequence_io.h:28,
from hisat2_build.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:478:56: 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:764:63: 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 gfm.h:43,
from hisat2_build.cpp:35:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 hisat2_build.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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from hisat2_build.cpp:35:
gfm.h: In instantiation of ‘void GFM<index_t>::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool) [with TStr = SString<char>; index_t = long long unsigned int; std::string = std::__cxx11::basic_string<char>; std::ofstream = std::basic_ofstream<char>; uint32_t = unsigned int]’:
gfm.h:955:3: required from ‘GFM<index_t>::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, 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]’
hgfm.h:1970:14: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: required from here
gfm.h:1929:102: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
1929 | std::numeric_limits<index_t>::max(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_sw_driver.h:86,
from hi_aligner.h:42,
from spliced_aligner.h:23,
from hisat2.cpp:45:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_sw_driver.h:86,
from hi_aligner.h:42,
from spliced_aligner.h:23,
from hisat2.cpp:45:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from gfm.h:43,
from hisat2_build.cpp:35:
blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’:
blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA<TStr>::nextBlock(int, int) [with TStr = SString<char>]’
blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = SString<char>; TIndexOffU = long long unsigned int]’
hgfm.h:1833:55: required from ‘static void HGFM<index_t, local_index_t>::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hgfm.h:2180:26: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: required from here
blockwise_sa.h:453:15: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
453 | mkeyQSortSuf(t, s, slen, 4,
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~
454 | this->verbose(), this->sanityCheck());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
blockwise_sa.h:453:15: 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 gfm.h:43,
from hisat2_build.cpp:35:
diff_sample.h: In instantiation of ‘void DifferenceCoverSample<T>::build(int) [with TStr = SString<char>]’:
blockwise_sa.h:375:4: required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:354:4: required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:206:29: 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>]’
hgfm.h:1820:55: required from ‘static void HGFM<index_t, local_index_t>::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hgfm.h:2180:26: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: 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]
In file included from ds.h:32,
from sequence_io.h:28,
from hisat2_build.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 = SString<char>; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA<TStr>::nextBlock(int, int) [with TStr = SString<char>]’
blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = SString<char>; TIndexOffU = long long unsigned int]’
hgfm.h:1833:55: required from ‘static void HGFM<index_t, local_index_t>::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hgfm.h:2180:26: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: 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:764:63: 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 gfm.h:43,
from hisat2_build.cpp:35:
multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
blockwise_sa.h:453:15: required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA<TStr>::nextBlock(int, int) [with TStr = SString<char>]’
blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = SString<char>; TIndexOffU = long long unsigned int]’
hgfm.h:1833:55: required from ‘static void HGFM<index_t, local_index_t>::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hgfm.h:2180:26: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: required from here
multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
multikey_qsort.h: In instantiation of ‘void 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:375:4: required from ‘void KarkkainenBlockwiseSA<TStr>::build() [with TStr = SString<char>]’
blockwise_sa.h:354:4: required from ‘void KarkkainenBlockwiseSA<TStr>::reset() [with TStr = SString<char>]’
blockwise_sa.h:206:29: 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>]’
hgfm.h:1820:55: required from ‘static void HGFM<index_t, local_index_t>::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hgfm.h:2180:26: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: required from here
multikey_qsort.h:661:31: 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 hisat2_build.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 = 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:447:19: required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA<TStr>::nextBlock(int, int) [with TStr = SString<char>]’
blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = SString<char>; TIndexOffU = long long unsigned int]’
hgfm.h:1833:55: required from ‘static void HGFM<index_t, local_index_t>::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hgfm.h:2180:26: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1753:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1753 | auto_ptr<Presets> presets(new PresetsV0());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1753:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1753 | auto_ptr<Presets> presets(new PresetsV0());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
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:1166:20: 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:447:19: required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA<TStr>::nextBlock(int, int) [with TStr = SString<char>]’
blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = SString<char>; TIndexOffU = long long unsigned int]’
hgfm.h:1833:55: required from ‘static void HGFM<index_t, local_index_t>::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hgfm.h:2180:26: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:447:19: required from ‘void KarkkainenBlockwiseSA<TStr>::qsort(EList<long long unsigned int>&) [with TStr = SString<char>]’
blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA<TStr>::nextBlock(int, int) [with TStr = SString<char>]’
blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = SString<char>; TIndexOffU = long long unsigned int]’
hgfm.h:1833:55: required from ‘static void HGFM<index_t, local_index_t>::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hgfm.h:2180:26: required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:687:142: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3068:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3068 | auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp:3069:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3069 | auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3068:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3068 | auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp:3085:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3085 | auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp:3069:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3069 | auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp:3085:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3085 | auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’:
hisat2.cpp:3826:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3826 | auto_ptr<BitPairReference> refs(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’:
hisat2.cpp:3826:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3826 | auto_ptr<BitPairReference> refs(
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2.cpp:33:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
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 gfm.h:43,
from hgfm.h:24,
from hisat2.cpp:33:
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:478:56: 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:764:63: 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 gfm.h:43,
from hgfm.h:24,
from hisat2.cpp:33:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 gfm.h:43,
from hgfm.h:24,
from hisat2.cpp:33:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from hgfm.h:24,
from hisat2.cpp:33:
gfm.h: In instantiation of ‘void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = unsigned int]’:
hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2.cpp:4115:51: required from here
gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
6451 | int lastorig = -1;
| ^~~~~~~~
In file included from hgfm.h:24,
from hisat2.cpp:33:
gfm.h: In instantiation of ‘void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = long long unsigned int]’:
hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2.cpp:4115:51: required from here
gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
6451 | int lastorig = -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 gfm.h:43,
from hgfm.h:24,
from hisat2.cpp:33:
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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | OFF_MASK, begin, end);
| ^~~~~~~~
In file included from spliced_aligner.h:23,
from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’:
hi_aligner.h:4796:54: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
hi_aligner.h:2125:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare]
2125 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~
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 gfm.h:43,
from hgfm.h:24,
from hisat2.cpp:33:
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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from aligner_seed2.h:109,
from aligner_driver.h:78,
from hi_aligner.h:41,
from spliced_aligner.h:23,
from hisat2.cpp:45:
group_walk.h: In instantiation of ‘std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’:
group_walk.h:1542:4: required from ‘bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]’
hi_aligner.h:5003:9: required from ‘bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4773:17: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1172 | if(new_node_bot - new_node_top < gws.map.size()) {
In file included from aligner_seed2.h:109,
from aligner_driver.h:78,
from hi_aligner.h:41,
from spliced_aligner.h:23,
from hisat2.cpp:45:
group_walk.h: In instantiation of ‘std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’:
group_walk.h:1542:4: required from ‘bool GroupWalk2S<index_t, T, S>::advanceElement(index_t, const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GroupWalkState<index_t>&, WalkResult<index_t>&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]’
hi_aligner.h:5003:9: required from ‘bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4773:17: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1172 | if(new_node_bot - new_node_top < gws.map.size()) {
group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1183 | for(index_t j = 0; j + 1 < gws.map.size(); j++) {
group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1183 | for(index_t j = 0; j + 1 < gws.map.size(); j++) {
group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1238 | if(node_range.second - node_range.first < st.back().map_.size()) {
group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1238 | if(node_range.second - node_range.first < st.back().map_.size()) {
group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1249 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) {
group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1249 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) {
In file included from spliced_aligner.h:23,
from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’:
hi_aligner.h:706:28: required from ‘static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:2194:47: required from ‘static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’
hi_aligner.h:4796:54: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2625 | if(rfoff >= contig_len) return 0;
| ~~~~~~^~~~~~~~~~~~~
In file included from spliced_aligner.h:23,
from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’:
hi_aligner.h:706:28: required from ‘static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:2194:47: required from ‘static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’
hi_aligner.h:4796:54: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2625 | if(rfoff >= contig_len) return 0;
| ~~~~~~^~~~~~~~~~~~~
hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2703 | if(alt_range.first >= alts.size()) {
hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2703 | if(alt_range.first >= alts.size()) {
hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
2868 | for(int i = 0; i < alt.len; i++) {
| ~~^~~~~~~~~
hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2868 | for(int i = 0; i < alt.len; i++) {
| ~~^~~~~~~~~
hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
2909 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) {
| ~~~~~^~~~~~~~
hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
2909 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) {
| ~~~~~^~~~~~~~
hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
2985 | if(alignedLen == next_rdlen) return rdlen;
| ~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2985 | if(alignedLen == next_rdlen) return rdlen;
| ~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
3021 | if(mm_max_rd_i + rdoff > best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
3021 | if(mm_max_rd_i + rdoff > best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
3026 | } else if(mm_max_rd_i + rdoff == best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
3026 | } else if(mm_max_rd_i + rdoff == best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
3278 | if(best_rdoff < rdoff + rd_i) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
3278 | if(best_rdoff < rdoff + rd_i) {
| ~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from aligner_seed2.h:109,
from aligner_driver.h:78,
from hi_aligner.h:41,
from spliced_aligner.h:23,
from hisat2.cpp:45:
group_walk.h: In instantiation of ‘std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’:
group_walk.h:492:66: required from ‘std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’
group_walk.h:1478:3: required from ‘void GroupWalk2S<index_t, T, S>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]’
hi_aligner.h:4998:5: required from ‘bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4773:17: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
794 | while(new_top - top < tmp_gbwt_to_node.size()) {
In file included from aligner_seed2.h:109,
from aligner_driver.h:78,
from hi_aligner.h:41,
from spliced_aligner.h:23,
from hisat2.cpp:45:
group_walk.h: In instantiation of ‘std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’:
group_walk.h:492:66: required from ‘std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, index_t, index_t, index_t, index_t, const EList<std::pair<_FIter, _FIter> >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’
group_walk.h:1478:3: required from ‘void GroupWalk2S<index_t, T, S>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice<short unsigned int, 16>; int S = 16]’
hi_aligner.h:4998:5: required from ‘bool HI_Aligner<index_t, local_index_t>::getGenomeCoords_local(const GFM<local_index_t>&, const ALTDB<index_t>&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList<std::pair<index_t, index_t> >&, bool, index_t, index_t, EList<Coord>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4773:17: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
794 | while(new_top - top < tmp_gbwt_to_node.size()) {
group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
801 | if(new_top - top == tmp_gbwt_to_node.size()) {
group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
801 | if(new_top - top == tmp_gbwt_to_node.size()) {
group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
817 | if(i + 1 < tmp_zOffs.size()) {
group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
817 | if(i + 1 < tmp_zOffs.size()) {
group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
823 | while(new_bot2 - top < tmp_gbwt_to_node.size()) {
group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
823 | while(new_bot2 - top < tmp_gbwt_to_node.size()) {
group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
830 | if(new_bot2 - top < tmp_gbwt_to_node.size()) {
group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
830 | if(new_bot2 - top < tmp_gbwt_to_node.size()) {
In file included from spliced_aligner.h:23,
from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, Haplotype<index_t>&, EList<std::pair<_FIter, _FIter> >&, index_t, bool, bool) [with index_t = unsigned int]’:
hi_aligner.h:2739:39: required from ‘static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:706:28: required from ‘static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:2194:47: required from ‘static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’
hi_aligner.h:4796:54: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2484 | if(ht_range.first >= haplotypes.size())
hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2499 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from spliced_aligner.h:23,
from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, Haplotype<index_t>&, EList<std::pair<_FIter, _FIter> >&, index_t, bool, bool) [with index_t = long long unsigned int]’:
hi_aligner.h:2739:39: required from ‘static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:706:28: required from ‘static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:2194:47: required from ‘static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’
hi_aligner.h:4796:54: required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:3926:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3435:151: required from here
hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2484 | if(ht_range.first >= haplotypes.size())
hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
2499 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2537 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
2537 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2561 | for(; ht_range.second < haplotypes.size(); ht_range.second++) {
hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2561 | for(; ht_range.second < haplotypes.size(); ht_range.second++) {
hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2568 | if(ht_list[h].first == ht_range.second) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
2568 | if(ht_list[h].first == ht_range.second) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from hisat2.cpp:45:
spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’:
spliced_aligner.h:214:9: required from here
spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable]
282 | bool another_spliced = false;
| ^~~~~~~~~~~~~~~
In file included from hisat2.cpp:45:
spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’:
spliced_aligner.h:214:9: required from here
spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable]
282 | bool another_spliced = false;
| ^~~~~~~~~~~~~~~
spliced_aligner.h:642:65: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare]
642 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) {
spliced_aligner.h:1298:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare]
1298 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) {
In file included from spliced_aligner.h:23,
from hisat2.cpp:45:
hi_aligner.h: In instantiation of ‘index_t HI_Aligner<index_t, local_index_t>::globalGFMSearch(const GFM<index_t>&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList<std::pair<_FIter, _FIter> >&, RandomSource&, bool&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’:
spliced_aligner.h:936:25: required from ‘int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’
spliced_aligner.h:214:9: required from here
hi_aligner.h:5792:85: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
5792 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/9/set:60,
from gfm.h:32,
from hisat2_build.cpp:35:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, long long unsigned int> >’} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from gbwt_graph.h:28,
from gfm.h:64,
from hisat2_build.cpp:35:
/usr/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, long long unsigned int> >]’:
/usr/include/c++/9/bits/stl_map.h:499:8: 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’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, long long unsigned int> >’} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/set:60,
from gfm.h:32,
from hisat2_build.cpp:35:
/usr/include/c++/9/bits/stl_tree.h: In member 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++/9/bits/stl_tree.h:2452:7: 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’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, long long unsigned int> >’} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from gbwt_graph.h:28,
from gfm.h:64,
from hisat2_build.cpp:35:
/usr/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less<long long unsigned int>; _Alloc = std::allocator<std::pair<const long long unsigned int, long long unsigned int> >]’:
/usr/include/c++/9/bits/stl_map.h:499:8: 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’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, long long unsigned int> >’} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/set:60,
from gfm.h:32,
from hisat2_build.cpp:35:
/usr/include/c++/9/bits/stl_tree.h: In member 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 std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, long long unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> >]’:
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long unsigned int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> >’} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from gbwt_graph.h:28,
from gfm.h:64,
from hisat2_build.cpp:35:
/usr/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Tp = long long unsigned int; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> >]’:
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, long long unsigned int>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, long long unsigned int> >’} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/set:60,
from gfm.h:32,
from hisat2_build.cpp:35:
/usr/include/c++/9/bits/stl_tree.h: In member 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 RefGraph<long long unsigned int>::CompositeNodeIDs&>, std::tuple<>}; _Key = RefGraph<long long unsigned int>::CompositeNodeIDs; _Val = std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int>; _KeyOfValue = std::_Select1st<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> >; _Compare = std::less<RefGraph<long long unsigned int>::CompositeNodeIDs>; _Alloc = std::allocator<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> >]’:
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree<RefGraph<long long unsigned int>::CompositeNodeIDs, std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int>, std::_Select1st<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> >, std::less<RefGraph<long long unsigned int>::CompositeNodeIDs>, std::allocator<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> >’} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from gbwt_graph.h:28,
from gfm.h:64,
from hisat2_build.cpp:35:
/usr/include/c++/9/bits/stl_map.h: In static member function ‘static void RefGraph<index_t>::reverseDeterminize(EList<RefGraph<index_t>::Node>&, EList<RefGraph<index_t>::Edge>&, index_t&, index_t) [with index_t = long long unsigned int]’:
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree<RefGraph<long long unsigned int>::CompositeNodeIDs, std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int>, std::_Select1st<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> >, std::less<RefGraph<long long unsigned int>::CompositeNodeIDs>, std::allocator<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> >’} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree<RefGraph<long long unsigned int>::CompositeNodeIDs, std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int>, std::_Select1st<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> >, std::less<RefGraph<long long unsigned int>::CompositeNodeIDs>, std::allocator<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const RefGraph<long long unsigned int>::CompositeNodeIDs, long long unsigned int> >’} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In constructor ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long long unsigned int; local_index_t = short unsigned int]’:
/usr/include/c++/9/bits/stl_map.h:499:8: 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’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, long long unsigned int> >’} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: 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’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const long long unsigned int, long long unsigned int> >’} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from edit.h:29,
from edit.cpp:21:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 edit.h:29,
from edit.cpp:21:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
456 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
450 | bool binarySearched = false;
| ^~~~~~~~~~~~~~
In file included from gfm.h:43,
from gfm.cpp:21:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
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 gfm.h:43,
from gfm.cpp:21:
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:478:56: 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:764:63: 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 gfm.h:43,
from gfm.cpp:21:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 gfm.h:43,
from gfm.cpp:21:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
456 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
450 | bool binarySearched = false;
| ^~~~~~~~~~~~~~
/usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \
-DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"04 January 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \
-I third_party -I . \
-o hisat2-inspect-s hisat2_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread -Wl,-z,relro -Wl,-z,now
In file included from hisat2_inspect.cpp:25:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
227 | if(!((a) <= (b))) { \
| ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
180 | assert_leq(fw, 1);
| ^~~~~~~~~~
In file included from hgfm.h:24,
from hisat2_inspect.cpp:27:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2_inspect.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from hgfm.h:24,
from hisat2_inspect.cpp:27:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2_inspect.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
/usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \
-DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"04 January 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \
-I third_party -I . \
-o hisat2-inspect-l hisat2_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread -Wl,-z,relro -Wl,-z,now
make[2]: Nothing to be done for 'doc'.
In file included from gfm.h:43,
from hgfm.h:24,
from hisat2_inspect.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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from hisat2_inspect.cpp:25:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
227 | if(!((a) <= (b))) { \
| ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
180 | assert_leq(fw, 1);
| ^~~~~~~~~~
In file included from hgfm.h:24,
from hisat2_inspect.cpp:27:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2_inspect.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from hgfm.h:24,
from hisat2_inspect.cpp:27:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from hgfm.h:24,
from hisat2_inspect.cpp:27:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
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 gfm.h:43,
from hgfm.h:24,
from hisat2_inspect.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:478:56: 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:764:63: 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 gfm.h:43,
from hgfm.h:24,
from hisat2_inspect.cpp:27:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 gfm.h:43,
from hgfm.h:24,
from hisat2_inspect.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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from edit.h:29,
from edit.cpp:21:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 edit.h:29,
from edit.cpp:21:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
456 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
450 | bool binarySearched = false;
| ^~~~~~~~~~~~~~
In file included from gfm.h:43,
from gfm.cpp:21:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
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 gfm.h:43,
from gfm.cpp:21:
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:478:56: 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:764:63: 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 gfm.h:43,
from gfm.cpp:21:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 gfm.h:43,
from gfm.cpp:21:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
456 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
450 | bool binarySearched = false;
| ^~~~~~~~~~~~~~
In file included from edit.h:26,
from edit.cpp:21:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
227 | if(!((a) <= (b))) { \
| ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
180 | assert_leq(fw, 1);
| ^~~~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from edit.h:26,
from edit.cpp:21:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
227 | if(!((a) <= (b))) { \
| ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
180 | assert_leq(fw, 1);
| ^~~~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from edit.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from edit.h:29,
from edit.cpp:21:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from edit.cpp:21:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 edit.h:29,
from edit.cpp:21:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from alphabet.h:27,
from gfm.h:40,
from gfm.cpp:21:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
227 | if(!((a) <= (b))) { \
| ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
180 | assert_leq(fw, 1);
| ^~~~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.h:43,
from gfm.cpp:21:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from alphabet.h:27,
from gfm.h:40,
from gfm.cpp:21:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
227 | if(!((a) <= (b))) { \
| ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
180 | assert_leq(fw, 1);
| ^~~~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/memory:80,
from gfm.h:28,
from gfm.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
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 gfm.h:43,
from gfm.cpp:21:
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:478:56: 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:764:63: 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 gfm.h:43,
from gfm.cpp:21:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 gfm.h:43,
from gfm.cpp:21:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from aligner_cache.h:59,
from aligner_seed.cpp:20:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_seed.h:30,
from aligner_seed.cpp:21:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from aligner_cache.h:59,
from aligner_seed.cpp:20:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_sw.cpp:25:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from random_util.h:25,
from aligner_seed2.h:101,
from aligner_seed2.cpp:22:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_seed2.cpp:22:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 random_util.h:25,
from aligner_seed2.h:101,
from aligner_seed2.cpp:22:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_sw.cpp:25:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.cpp:25:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_sw.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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from aligner_result.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from aligner_result.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from aligner_result.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from aligner_result.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from ref_read.h:33,
from reference.h:32,
from aligner_result.cpp:21:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_result.cpp:22:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 ref_read.h:33,
from reference.h:32,
from aligner_result.cpp:21:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from aln_sink.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from aln_sink.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from aln_sink.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from aln_sink.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from read.h:25,
from aln_sink.h:24,
from aln_sink.cpp:22:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from aln_sink.h:25,
from aln_sink.cpp:22:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aln_sink.h:24,
from aln_sink.cpp:22:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from read.h:25,
from aligner_result.h:27,
from unique.h:38,
from unique.cpp:20:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from unique.h:38,
from unique.cpp:20:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aligner_result.h:27,
from unique.h:38,
from unique.cpp:20:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_bt.h:31,
from aligner_bt.cpp:20:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_bt.h:31,
from aligner_bt.cpp:20:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_bt.h:25,
from aligner_bt.cpp:20:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from sse_util.cpp:20:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_swsse.cpp:22:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from sse_util.cpp:20:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_swsse.cpp:22:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_swsse.cpp:21:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_swsse_loc_i16.cpp:56:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_swsse_loc_i16.cpp:56:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_i16.cpp:56:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_swsse_ee_i16.cpp:56:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_swsse_ee_i16.cpp:56:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_i16.cpp:56:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_swsse_loc_u8.cpp:56:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_swsse_loc_u8.cpp:56:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_loc_u8.cpp:56:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_swsse_ee_u8.cpp:56:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from aligner_swsse.h:28,
from aligner_sw.h:84,
from aligner_swsse_ee_u8.cpp:56:
sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’:
sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=]
220 | last_alloc_ = new simde__m128i[sz + 2];
| ^
sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter
sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support
In file included from ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:74,
from aligner_swsse_ee_u8.cpp:56:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from splice_site.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from splice_site.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM<unsigned int>&, const EList<ALT<unsigned int> >&)’:
splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context]
717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from edit.h:29,
from splice_site.cpp:20:
ds.h: In instantiation of ‘void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = unsigned int]’:
splice_site.cpp:722:59: required from here
ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
663 | std::memcpy(list_ + cur_, l, bytes);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from edit.h:30,
from splice_site.cpp:20:
splice_site.h:377:7: note: ‘class Exon’ declared here
377 | class Exon {
| ^~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from ds.h:32,
from random_util.h:25,
from aligner_seed2.h:101,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from aligner_result.h:30,
from aligner_seed2.h:102,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 random_util.h:25,
from aligner_seed2.h:101,
from aligner_driver.h:78,
from aligner_driver.cpp:20:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
In file included from gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
484 | 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:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
In file included from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1098:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1098 | auto_ptr<stringstream> ss(new stringstream());
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from splice_site.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
gfm.h:1102:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1102 | auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
| ^~~~~~~~
In file included from /usr/include/c++/9/bits/locale_conv.h:41,
from /usr/include/c++/9/locale:43,
from /usr/include/c++/9/iomanip:43,
from timer.h:26,
from reference.h:36,
from splice_site.h:32,
from edit.h:30,
from splice_site.cpp:20:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM<long long unsigned int>&, const EList<ALT<long long unsigned int> >&)’:
splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context]
717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from ds.h:32,
from edit.h:29,
from splice_site.cpp:20:
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:478:56: 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:764:63: 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 gfm.h:43,
from splice_site.h:34,
from edit.h:30,
from splice_site.cpp:20:
multikey_qsort.h:764:40: 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:764:40: 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:484:52: required from here
multikey_qsort.h:496:40: 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 edit.h:29,
from splice_site.cpp:20:
ds.h: In instantiation of ‘void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = unsigned int]’:
splice_site.cpp:722:59: required from here
ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
663 | std::memcpy(list_ + cur_, l, bytes);
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from edit.h:30,
from splice_site.cpp:20:
splice_site.h:377:7: note: ‘class Exon’ declared here
377 | class Exon {
| ^~~~
In file included from ds.h:32,
from edit.h:29,
from splice_site.cpp:20:
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:478:56: 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:1160:49: note: in expansion of macro ‘OFF_MASK’
1160 | 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:1169:49: note: in expansion of macro ‘OFF_MASK’
1169 | 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:1166:20: 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:478:56: 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:1071:40: note: in expansion of macro ‘OFF_MASK’
1071 | 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:1067:33: 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:1166:20: 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:478:56: 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:914:10: 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:923:29: 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:1007:48: note: in expansion of macro ‘OFF_MASK’
1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end);
| ^~~~~~~~
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
help2man ./hisat2 --no-info --name \
'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \
> debian/hisat2.1
help2man ./hisat2-align-l --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, large index binary' \
--no-info > debian/hisat2-align-l.1
help2man ./hisat2-align-s --name 'HISAT2 graph-based alignment of short nucleotide reads to many genomes, small index binary' \
--no-info > debian/hisat2-align-s.1
help2man ./hisat2-build --name 'HISAT2 indexer, wrapper script' \
--no-info > debian/hisat2-build.1
#rm hisat2-buildc
help2man ./hisat2-build-l --name 'HISAT2 indexer, large index binary' \
--no-info > debian/hisat2-build-l.1
help2man ./hisat2-build-s --name 'HISAT2 indexer, small index binary' \
--no-info > debian/hisat2-build-s.1
help2man ./hisat2-inspect --name 'HISAT2 index inspector, wrapper script' \
--no-info > debian/hisat2-inspect.1
help2man ./hisat2-inspect-l --name 'HISAT2 index inspector, large index binary' \
--no-info > debian/hisat2-inspect-l.1
help2man ./hisat2-inspect-s --name 'HISAT2 index inspector, small index binary' \
--no-info > debian/hisat2-inspect-s.1
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_test -a
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
for pl in `grep -Rl '#!/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_installdocs -a
dh_installchangelogs -a
dh_installexamples -a
dh_installman -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/hisat2/usr/bin/hisat2-inspect-s contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-inspect-l contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-align-l contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-build-s contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-align-s contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/hisat2/usr/bin/hisat2-build-l 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/hisat2/usr/bin/hisat2-inspect-s debian/hisat2/usr/bin/hisat2-inspect-l debian/hisat2/usr/bin/hisat2-align-l debian/hisat2/usr/bin/hisat2-build-s debian/hisat2/usr/bin/hisat2-align-s debian/hisat2/usr/bin/hisat2-build-l were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'hisat2' in '../hisat2_2.1.0-2nopython3hisat3_armhf.deb'.
dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.1.0-2nopython3hisat3_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> >../hisat2_2.1.0-2nopython3hisat3_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 2020-01-07T16:07:56Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
hisat2_2.1.0-2nopython3hisat3_armhf.changes:
--------------------------------------------
Format: 1.8
Date: Sat, 04 Jan 2020 22:52:02 +0100
Source: hisat2
Binary: hisat2 hisat2-dbgsym
Architecture: armhf
Version: 2.1.0-2nopython3hisat3
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Michael R. Crusoe <michael.crusoe@gmail.com>
Description:
hisat2 - graph-based alignment of short nucleotide reads to many genomes
Changes:
hisat2 (2.1.0-2nopython3hisat3) unstable; urgency=medium
.
* armhf armel ppc64el s390x: add -Wno-narrowing
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Files:
87baf85bdc3c8e67360e3494cbbb6f7b 9339564 debug optional hisat2-dbgsym_2.1.0-2nopython3hisat3_armhf.deb
3cda4cc6ae21fb92a4777e6cb0ec1de5 5104 science optional hisat2_2.1.0-2nopython3hisat3_armhf.buildinfo
1708ff1cd4e1f75654dd056670d22851 3078572 science optional hisat2_2.1.0-2nopython3hisat3_armhf.deb
+------------------------------------------------------------------------------+
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hisat2-dbgsym_2.1.0-2nopython3hisat3_armhf.deb
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new Debian package, version 2.0.
size 9339564 bytes: control archive=856 bytes.
602 bytes, 12 lines control
722 bytes, 7 lines md5sums
Package: hisat2-dbgsym
Source: hisat2
Version: 2.1.0-2nopython3hisat3
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 9573
Depends: hisat2 (= 2.1.0-2nopython3hisat3)
Section: debug
Priority: optional
Description: debug symbols for hisat2
Build-Ids: 82069ffabaabaa9170f1a948695d486368514bdf 8923dd180a55030f53b8c50f85fbfcd1db95a605 8cfd733168506c7cb17f62560e6e9660da8ac35f 9e17e79919dad7d1139d10c12d27074949904fc9 be900f4283483e2ffe5ba64a02125c4ca6bfcacd c05fbb6c87d2bd5c3323e712af72c75a727e29a0
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drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/lib/debug/
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drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 482176 2020-01-04 21:52 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/hisat2.debug
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/share/
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-01-04 21:52 ./usr/share/doc/hisat2-dbgsym -> hisat2
hisat2_2.1.0-2nopython3hisat3_armhf.deb
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new Debian package, version 2.0.
size 3078572 bytes: control archive=1828 bytes.
1278 bytes, 22 lines control
2420 bytes, 33 lines md5sums
Package: hisat2
Version: 2.1.0-2nopython3hisat3
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12186
Depends: libc6 (>= 2.29), libgcc1 (>= 1:3.5), libstdc++6 (>= 9), perl:any, python3
Recommends: python3-hisat2, bcftools, samtools
Section: science
Priority: optional
Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml
Description: graph-based alignment of short nucleotide reads to many genomes
HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as against a single reference genome). Based on an extension of BWT for graphs
a graph FM index (GFM) was designed and implementd. In addition to using
one global GFM index that represents a population of human genomes, HISAT2
uses a large set of small GFM indexes that collectively cover the whole genome
(each index representing a genomic region of 56 Kbp, with 55,000 indexes
needed to cover the human population). These small indexes (called local
indexes), combined with several alignment strategies, enable rapid and
accurate alignment of sequencing reads. This new indexing scheme is called a
Hierarchical Graph FM index (HGFM).
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drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/bin/
-rwxr-xr-x root/root 18074 2020-01-04 21:52 ./usr/bin/hisat2
-rwxr-xr-x root/root 1423236 2020-01-04 21:52 ./usr/bin/hisat2-align-l
-rwxr-xr-x root/root 1398660 2020-01-04 21:52 ./usr/bin/hisat2-align-s
-rwxr-xr-x root/root 2808 2020-01-04 21:52 ./usr/bin/hisat2-build
-rwxr-xr-x root/root 639592 2020-01-04 21:52 ./usr/bin/hisat2-build-l
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-rwxr-xr-x root/root 321264 2020-01-04 21:52 ./usr/bin/hisat2-inspect-s
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/share/
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/share/doc/hisat2/
-rw-r--r-- root/root 20100 2017-06-07 19:17 ./usr/share/doc/hisat2/MANUAL.gz
-rw-r--r-- root/root 1029 2020-01-04 21:52 ./usr/share/doc/hisat2/changelog.Debian.gz
-rw-r--r-- root/root 2321 2019-12-29 18:17 ./usr/share/doc/hisat2/copyright
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/share/doc/hisat2/examples/
drwxr-xr-x root/root 0 2017-06-07 19:32 ./usr/share/doc/hisat2/examples/index/
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-rw-r--r-- root/root 37688 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/index/22_20-21M_snp.8.ht2
drwxr-xr-x root/root 0 2017-06-07 19:32 ./usr/share/doc/hisat2/examples/reads/
-rw-r--r-- root/root 105893 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/reads/reads_1.fa
-rw-r--r-- root/root 105893 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/reads/reads_2.fa
drwxr-xr-x root/root 0 2017-06-07 19:32 ./usr/share/doc/hisat2/examples/reference/
-rw-r--r-- root/root 1016689 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/reference/22_20-21M.fa
-rw-r--r-- root/root 167831 2015-09-08 11:39 ./usr/share/doc/hisat2/examples/reference/22_20-21M.snp
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/share/man/
drwxr-xr-x root/root 0 2020-01-04 21:52 ./usr/share/man/man1/
-rw-r--r-- root/root 2714 2020-01-04 21:52 ./usr/share/man/man1/hisat2-align-l.1.gz
-rw-r--r-- root/root 2713 2020-01-04 21:52 ./usr/share/man/man1/hisat2-align-s.1.gz
-rw-r--r-- root/root 1133 2020-01-04 21:52 ./usr/share/man/man1/hisat2-build-l.1.gz
-rw-r--r-- root/root 1131 2020-01-04 21:52 ./usr/share/man/man1/hisat2-build-s.1.gz
-rw-r--r-- root/root 1186 2020-01-04 21:52 ./usr/share/man/man1/hisat2-build.1.gz
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-rw-r--r-- root/root 2915 2020-01-04 21:52 ./usr/share/man/man1/hisat2.1.gz
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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: 92560
Build-Time: 440
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 178
Job: hisat2_2.1.0-2nopython3hisat3
Machine Architecture: armhf
Package: hisat2
Package-Time: 643
Source-Version: 2.1.0-2nopython3hisat3
Space: 92560
Status: successful
Version: 2.1.0-2nopython3hisat3
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Finished at 2020-01-07T16:07:56Z
Build needed 00:10:43, 92560k disk space