hisat2 →
2.2.0-2 →
armhf → 2020-05-09 05:38:41
sbuild (Debian sbuild) 0.73.0 (23 Dec 2016) on test2019
+==============================================================================+
| hisat2 2.2.0-2 (armhf) Sat, 09 May 2020 05:03:12 +0000 |
+==============================================================================+
Package: hisat2
Version: 2.2.0-2
Source Version: 2.2.0-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
Build Type: any
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-8e2a6052-8f19-4756-9705-9694dc36cf74' 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 [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 21s (1143 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| 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 6922 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main hisat2 2.2.0-2 (dsc) [2111 B]
Get:2 http://172.17.0.1/private bullseye-staging/main hisat2 2.2.0-2 (tar) [6867 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main hisat2 2.2.0-2 (diff) [52.5 kB]
Fetched 6922 kB in 2s (3535 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hisat2-dQpKDF/hisat2-2.2.0' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hisat2-dQpKDF' 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-inptEl/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-inptEl/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-inptEl/gpg/trustdb.gpg: trustdb created
gpg: key E70254B6505CF8F7: 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 E70254B6505CF8F7: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key E70254B6505CF8F7: 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-inptEl/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2908 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-inptEl/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
libpam-cap
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 16 not upgraded.
Need to get 856 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [856 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 856 B in 0s (37.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14084 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) ...
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 12), libsimde-dev, help2man, pandoc, python3:any
Filtered Build-Depends: debhelper-compat (= 12), libsimde-dev, help2man, pandoc, python3:any
dpkg-deb: building package 'sbuild-build-depends-hisat2-dummy' in '/<<BUILDDIR>>/resolver-inptEl/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-inptEl/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Sources [531 B]
Get:5 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Packages [598 B]
Fetched 2462 B in 1s (3524 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-inptEl/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY E70254B6505CF8F7
Reading package lists...
Install hisat2 build dependencies (apt-based resolver)
------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
libpam-cap
Use 'apt autoremove' to remove it.
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 libpython3.8-minimal
libpython3.8-stdlib libsigsegv2 libsimde-dev libssl1.1 libsub-override-perl
libtinfo5 libtool libuchardet0 libxml2 m4 man-db mime-support pandoc
pandoc-data po-debconf python3 python3-minimal python3.8 python3.8-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 python3.8-venv python3.8-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 libpython3.8-minimal
libpython3.8-stdlib libsigsegv2 libsimde-dev libssl1.1 libsub-override-perl
libtinfo5 libtool libuchardet0 libxml2 m4 man-db mime-support pandoc
pandoc-data po-debconf python3 python3-minimal python3.8 python3.8-minimal
sbuild-build-depends-hisat2-dummy sensible-utils
0 upgraded, 52 newly installed, 0 to remove and 16 not upgraded.
Need to get 43.9 MB of archives.
After this operation, 225 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-inptEl/apt_archive ./ sbuild-build-depends-hisat2-dummy 0.invalid.0 [888 B]
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 6.2-1 [318 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 1.5.2-2 [29.6 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1g-1 [1272 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.3~rc1-1 [751 kB]
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Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.3~rc1-1 [1627 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 2.4.2-3 [68.1 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.3~rc1-1 [1598 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.3~rc1-1 [415 kB]
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Get:20 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-3 [63.7 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 1:5.38-4 [262 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
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 2.69-11.1 [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 1:1.16.2-1 [775 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13 [184 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.0-1 [24.2 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.0-1 [14.8 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 2.64.2-1 [1158 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5 [592 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 13 [1002 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf help2man armhf 1.47.15 [181 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libsimde-dev all 0.0.0.git.20200424-1 [87.6 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf pandoc-data all 2.5-3 [349 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf pandoc armhf 2.5-3+b1 [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 (1.5.2-2) ...
Setting up libsimde-dev (0.0.0.git.20200424-1) ...
Setting up mime-support (3.64) ...
Setting up libmagic-mgc (1:5.38-4) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.64.2-1) ...
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Setting up libdebhelper-perl (13) ...
Setting up libmagic1:armhf (1:5.38-4) ...
Setting up gettext-base (0.19.8.1-10) ...
Setting up file (1:5.38-4) ...
Setting up libicu63:armhf (63.2-3) ...
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 (2.4.2-3) ...
Setting up pandoc-data (2.5-3) ...
Setting up libpython3.8-stdlib:armhf (3.8.3~rc1-1) ...
Setting up python3.8 (3.8.3~rc1-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-5) ...
Setting up liblocale-gettext-perl (1.07-4) ...
Setting up libpython3-stdlib:armhf (3.8.2-3) ...
Setting up libfile-stripnondeterminism-perl (1.8.0-1) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up python3 (3.8.2-3) ...
Setting up help2man (1.47.15) ...
Setting up pandoc (2.5-3+b1) ...
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 (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.8.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up automake (1:1.16.2-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up man-db (2.9.1-1) ...
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 debhelper (13) ...
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Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.30-4+rpi1) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.19.20-v7+ armhf (armv7l)
Toolchain package versions: binutils_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-10+rpi1 gcc-9_9.3.0-10+rpi1 libc6-dev_2.30-4+rpi1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200418-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.0.2 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+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_9.3.0-10+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.8.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-10+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200418-1+rpi1 gcc-9_9.3.0-10+rpi1 gcc-9-base_9.3.0-10+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 help2man_1.47.15 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-6 libapt-pkg6.0_2.0.2 libarchive-zip-perl_1.68-1 libasan5_9.3.0-10+rpi1 libassuan0_2.5.3-7 libatomic1_10-20200418-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-5+rpi1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-4+rpi1 libc-dev-bin_2.30-4+rpi1 libc6_2.30-4+rpi1 libc6-dev_2.30-4+rpi1 libcap-ng0_0.7.9-2.1+b1 libcap2_1:2.33-1 libcap2-bin_1:2.33-1 libcc1-0_10-20200418-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.0-1 libgcc-9-dev_9.3.0-10+rpi1 libgcc-s1_10-20200418-1+rpi1 libgcc1_1:10-20200418-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10-20200418-1+rpi1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.3.5-2 libldap-2.4-2_2.4.49+dfsg-4+rpi1 libldap-common_2.4.49+dfsg-4+rpi1 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.33-1 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_10.34-7 libpcre3_2:8.39-12 libperl5.28_5.28.1-6 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpython3-stdlib_3.8.2-3 libpython3.8-minimal_3.8.3~rc1-1 libpython3.8-stdlib_3.8.3~rc1-1 libreadline7_7.0-5 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsimde-dev_0.0.0.git.20200424-1 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-9-dev_9.3.0-10+rpi1 libstdc++6_10-20200418-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.5-1+rpi1 libtasn1-6_4.16.0-2 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10-20200418-1+rpi1 libuchardet0_0.0.6-3 libudev1_245.5-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 pandoc_2.5-3+b1 pandoc-data_2.5-3 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.28_5.28.1-6 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python3_3.8.2-3 python3-minimal_3.8.2-3 python3.8_3.8.3~rc1-1 python3.8-minimal_3.8.3~rc1-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 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_2.96-3 tar_1.30+dfsg-7 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed May 6 18:49:03 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./hisat2_2.2.0-2.dsc
dpkg-source: info: extracting hisat2 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking hisat2_2.2.0.orig.tar.gz
dpkg-source: info: unpacking hisat2_2.2.0-2.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
dpkg-source: info: applying fix-manual
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/112/bus
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
INVOCATION_ID=720b06fe9d064e5ca4b0c1eb263ac862
JOURNAL_STREAM=8:20551
LANG=en_GB.UTF-8
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=116
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-8e2a6052-8f19-4756-9705-9694dc36cf74
SCHROOT_UID=112
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
XDG_RUNTIME_DIR=/run/user/112
XDG_SESSION_ID=c49279
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package hisat2
dpkg-buildpackage: info: source version 2.2.0-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
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-repeat 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-repeat-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-repeat.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-repeat-debug.exe \
hisat2-src.zip hisat2-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
rm -rf .ht2lib-obj*
rm -f libhisat2lib*.a libhisat2lib*.so
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary-arch
dh binary-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="06 May 2020" all doc
make -j4 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=06 May 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 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"06 May 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. -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 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"06 May 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. -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 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"06 May 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. -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 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"06 May 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. -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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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 hisat2_build.cpp:35:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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 hisat2_build.cpp:35:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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&, const string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, bool) [with TStr = SString<char>; index_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ofstream = std::basic_ofstream<char>; uint32_t = unsigned int]’:
gfm.h:1023:3: 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&, const string&, bool, bool, index_t, index_t, index_t, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
hgfm.h:1989:14: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: required from here
gfm.h:2151:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable]
2151 | index_t template_len = 0;
| ^~~~~~~~~~~~
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&, const string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:1023:3: 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&, const string&, bool, bool, index_t, index_t, index_t, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:1989:14: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: required from here
gfm.h:2151:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable]
2151 | index_t template_len = 0;
| ^~~~~~~~~~~~
gfm.h:2326:106: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow]
2326 | std::numeric_limits<index_t>::max(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
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:1843:55: 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:2211:30: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: 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:1830:55: 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:2211:30: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: 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]
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1823:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1823 | 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;
| ^~~~~~~~
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:1843:55: 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:2211:30: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: 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: 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:1843:55: 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:2211:30: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: 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);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1823:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1823 | 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 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:1830:55: 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:2211:30: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: 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:1843:55: 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:2211:30: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: 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);
| ^~~~~~~~
hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3167:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3167 | 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:3168:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3168 | 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:3189:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3189 | 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 multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3167:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3167 | 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:3168:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3168 | 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:3189:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
3189 | 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;
| ^~~~~~~~
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:1843:55: 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:2211:30: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: 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);
| ^~~~~~~~
hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’:
hisat2.cpp:4035:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
4035 | 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:4035:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
4035 | 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;
| ^~~~~~~~
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:1843:55: 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:2211:30: 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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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:535:15: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56: 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 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 spliced_aligner.h:23,
from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits)
hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefId’ {aka ‘long long int’} [-Wsign-compare]
4404 | if(positions[p].first.tid != res.refid()) continue;
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare]
4405 | if(positions[p].first.toff + 1000 < res.refoff() ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare]
4406 | res.refoff() + 1000 < positions[p].first.toff) continue;
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits)
hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits)
hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits);
| ~~~~~~~~~~~~^~~~~~~~~~
hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits);
hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
4614 | if(sink.numBestUnp(rdi).first > rp.khits) {
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 spliced_aligner.h:23,
from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘bool HI_Aligner<index_t, local_index_t>::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’:
hi_aligner.h:4088:17: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare]
5990 | if(_repeatConcordant[r].first == left.off() &&
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare]
5991 | _repeatConcordant[r].second == left2.off()) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
hi_aligner.h: In instantiation of ‘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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) {
| ~~~~~^~~~~~~~~~~~
hi_aligner.h:5688:65: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare]
5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off())
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘TRefOff’ {aka ‘long long int’} [-Wsign-compare]
5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off())
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
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:3815:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2.cpp:4351:51: required from here
gfm.h:6919:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
6919 | 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 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:3815:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2.cpp:4351:51: required from here
gfm.h:6919:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
6919 | int lastorig = -1;
| ^~~~~~~~
In file included from spliced_aligner.h:23,
from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘index_t HI_Aligner<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long long unsigned int; local_index_t = short unsigned int]’:
hi_aligner.h:5525:23: required from ‘bool HI_Aligner<index_t, local_index_t>::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4080:31: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare]
5150 | if(coord.ref() == numeric_limits<index_t>::max())
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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:5692:54: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare]
2267 | 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:46:
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:1517:4: 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:5901:9: 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:5664:17: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1147 | if(new_node_bot - new_node_top < gws.map.size()) {
group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) {
group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1213 | if(node_range.second - node_range.first < st.back().map_.size()) {
group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) {
In file included from spliced_aligner.h:23,
from hisat2.cpp:46:
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:717:28: 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:2337:47: 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:5692:54: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2801 | if(rfoff >= contig_len) return 0;
| ~~~~~~^~~~~~~~~~~~~
hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2879 | if(alt_range.first >= alts.size()) {
hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
3044 | for(int i = 0; i < alt.len; i++) {
| ~~^~~~~~~~~
hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) {
| ~~~~~^~~~~~~~
hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
3161 | if(alignedLen == next_rdlen) return rdlen;
| ~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
3197 | if(mm_max_rd_i + rdoff > best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare]
3454 | 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:46:
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:1517:4: 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:5901:9: 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:5664:17: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1147 | if(new_node_bot - new_node_top < gws.map.size()) {
group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) {
group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1213 | if(node_range.second - node_range.first < st.back().map_.size()) {
group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) {
In file included from spliced_aligner.h:23,
from hisat2.cpp:46:
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:717:28: 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:2337:47: 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:5692:54: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2801 | if(rfoff >= contig_len) return 0;
| ~~~~~~^~~~~~~~~~~~~
hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2879 | if(alt_range.first >= alts.size()) {
hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
3044 | for(int i = 0; i < alt.len; i++) {
| ~~^~~~~~~~~
hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) {
| ~~~~~^~~~~~~~
hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
3161 | if(alignedLen == next_rdlen) return rdlen;
| ~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
3197 | if(mm_max_rd_i + rdoff > best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) {
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
3454 | 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:46:
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:494:66: 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:1453:3: 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:5896:5: 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:5664:17: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) {
group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
789 | if(new_top - top == tmp_gbwt_to_node.size()) {
group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
795 | if(i + 1 < tmp_zOffs.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_bot - top < tmp_gbwt_to_node.size()) {
In file included from spliced_aligner.h:23,
from hisat2.cpp:46:
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:2915:39: 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:717:28: 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:2337:47: 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:5692:54: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2660 | if(ht_range.first >= haplotypes.size())
hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
2675 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
2713 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) {
hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare]
2744 | if(ht_list[h].first == ht_range.second) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
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:46:
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:494:66: 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:1453:3: 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:5896:5: 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:5664:17: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) {
group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
789 | if(new_top - top == tmp_gbwt_to_node.size()) {
group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
795 | if(i + 1 < tmp_zOffs.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_bot - top < tmp_gbwt_to_node.size()) {
In file included from spliced_aligner.h:23,
from hisat2.cpp:46:
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:2915:39: 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:717:28: 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:2337:47: 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:5692:54: 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 RepeatDB<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:4107:39: required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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:3556:58: required from here
hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2660 | if(ht_range.first >= haplotypes.size())
hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2675 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2713 | if(ht_list[h].first == ht_range.first) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) {
hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
2744 | if(ht_list[h].first == ht_range.second) {
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from hisat2.cpp:46:
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 RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’:
spliced_aligner.h:331:9: required from here
spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable]
408 | bool another_spliced = false;
| ^~~~~~~~~~~~~~~
spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare]
782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) {
spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare]
1465 | 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:46:
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:1086:25: 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 RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’
spliced_aligner.h:331:9: required from here
hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare]
6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from hisat2.cpp:46:
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 RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’:
spliced_aligner.h:331:9: required from here
spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable]
408 | bool another_spliced = false;
| ^~~~~~~~~~~~~~~
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 repeat.h:26,
from gfm.h:59,
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 repeat.h:26,
from gfm.h:59,
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 repeat.h:26,
from gfm.h:59,
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 repeat.h:26,
from gfm.h:59,
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&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, 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 gfm.h:59,
from hgfm.h:24,
from hisat2.cpp:33:
repeat.h: In member function ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]’:
repeat.h:41:20: warning: ‘cmp.RepeatCoord<unsigned int>::fw’ may be used uninitialized in this function [-Wmaybe-uninitialized]
41 | if(fw != o.fw)
| ~~^~
repeat.h:43:26: warning: ‘cmp.RepeatCoord<unsigned int>::alleleID’ may be used uninitialized in this function [-Wmaybe-uninitialized]
43 | if(alleleID != o.alleleID)
| ~~^~~~~~~~
In file included from gfm.h:59,
from hgfm.h:24,
from hisat2.cpp:33:
repeat.h: In member function ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, 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]’:
repeat.h:41:20: warning: ‘cmp.RepeatCoord<long long unsigned int>::fw’ may be used uninitialized in this function [-Wmaybe-uninitialized]
41 | if(fw != o.fw)
| ~~^~
repeat.h:43:26: warning: ‘cmp.RepeatCoord<long long unsigned int>::alleleID’ may be used uninitialized in this function [-Wmaybe-uninitialized]
43 | if(alleleID != o.alleleID)
| ~~^~~~~~~~
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
522 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
516 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
522 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
516 | 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 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"06 May 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. -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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"06 May 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. -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
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
522 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
516 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
522 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
516 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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;
| ^~~~~~~~
/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 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"06 May 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. -I third_party \
-o hisat2-repeat hisat2_repeat.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 mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \
-lpthread -Wl,-z,relro -Wl,-z,now
make[2]: Nothing to be done for 'doc'.
In file included from gfm.h:43,
from hisat2_repeat.cpp:36:
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 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_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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 hisat2_repeat.cpp:36:
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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_repeat.cpp:31:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
In file included from hisat2_repeat.cpp:36:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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_repeat.cpp:31:
/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: 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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 ds.h:32,
from sequence_io.h:28,
from hisat2_repeat.cpp:29:
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_repeat.cpp:36:
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_repeat.cpp:29:
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 hisat2_repeat.cpp:36:
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]’
hisat2_repeat.cpp:697:32: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, bool, bool) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_repeat.cpp:857:93: 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_repeat.cpp:36:
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>]’
hisat2_repeat.cpp:681:45: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, bool, bool) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_repeat.cpp:857:93: 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_repeat.cpp:29:
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]’
hisat2_repeat.cpp:697:32: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, bool, bool) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_repeat.cpp:857:93: 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_repeat.cpp:36:
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]’
hisat2_repeat.cpp:697:32: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, bool, bool) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_repeat.cpp:857:93: 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>]’
hisat2_repeat.cpp:681:45: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, bool, bool) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_repeat.cpp:857:93: 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_repeat.cpp:29:
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]’
hisat2_repeat.cpp:697:32: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, bool, bool) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_repeat.cpp:857:93: 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 = 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]’
hisat2_repeat.cpp:697:32: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, bool, bool) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_repeat.cpp:857:93: 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]’
hisat2_repeat.cpp:697:32: required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, bool, bool, bool) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_repeat.cpp:857:93: 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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_sw.cpp:25:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_sw.cpp:25:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
522 | uint64_t origBufOff = bufOff;
| ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
516 | bool binarySearched = false;
| ^~~~~~~~~~~~~~
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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_sw.h:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_loc_i16.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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_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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_loc_i16.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_sw.cpp:25:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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_sw_common.h:23,
from aligner_sw.h:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_ee_i16.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_ee_i16.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_ee_i16.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_loc_u8.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_ee_u8.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_loc_u8.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_loc_i16.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_ee_u8.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_ee_u8.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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:80,
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:80,
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:80,
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:80,
from aligner_swsse_loc_u8.cpp:56:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:80,
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 ds.h:32,
from read.h:25,
from aligner_result.h:27,
from aligner_sw_common.h:23,
from aligner_sw.h:80,
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:80,
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:80,
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 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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);
| ^~~~~~~~
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 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 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:80,
from bit_packed_array.cpp:24:
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:80,
from bit_packed_array.cpp:24:
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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 bit_packed_array.cpp:23:
/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:80,
from bit_packed_array.cpp:24:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 bit_packed_array.cpp:23:
/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 aligner_sw_common.h:23,
from aligner_sw.h:80,
from bit_packed_array.cpp:24:
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:80,
from bit_packed_array.cpp:24:
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:80,
from bit_packed_array.cpp:24:
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:80,
from repeat_builder.cpp:26:
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:80,
from repeat_builder.cpp:26:
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:1169:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1169 | 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 repeat_builder.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:80,
from repeat_builder.cpp:26:
gfm.h:1173:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
1173 | 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 repeat_builder.cpp:25:
/usr/include/c++/9/bits/unique_ptr.h:53:28: note: declared here
53 | template<typename> class auto_ptr;
| ^~~~~~~~
repeat_builder.cpp: In function ‘std::string reverse_complement(const string&)’:
repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
88 | rev[i] = asc2dnacomp[nt];
| ^~
repeat_builder.cpp: In function ‘std::string reverseComplement(const string&)’:
repeat_builder.cpp:200:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
200 | rc.push_back(asc2dnacomp[str[si - 1]]);
| ^
repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’:
repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
403 | for(size_t i = 0; i < num_cached_; i++) {
| ~~^~~~~~~~~~~~~
repeat_builder.cpp: In function ‘size_t extract_kmer(const string&, size_t, size_t)’:
repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]];
| ^
repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’:
repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
1225 | kmer = (kmer << 2) | asc2dna[base];
| ^~~~
repeat_builder.cpp: In function ‘void find_gap_pos(const string&, const string&, EList<unsigned int>&, EList<unsigned int>&, bool, size_t, size_t, size_t&, size_t&, bool)’:
repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1275 | for(int i = seq_len - 1; i >= gap_len; i--) {
| ~~^~~~~~~~~~
repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare]
1277 | if(i == seq_len - 1) ed2[i] = add;
| ~~^~~~~~~~~~~~~~
repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const string&, const string&, std::string&, size_t)’:
repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2915 | pad[i] = "CGTA"[asc2dna[ref[i]]];
| ^
repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2919 | pad[i] = "CGTA"[asc2dna[pad[i]]];
| ^
repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
2926 | for(size_t i = 0; i < head_len; i++) {
| ~~^~~~~~~~~~
repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts]
2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]];
| ^
repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const string&, const string&, EList<Edit>&, Coord&)’:
repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable]
3065 | int max_match_len = 0;
| ^~~~~~~~~~~~~
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:80,
from repeat_builder.cpp:26:
multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample<T1>&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’:
blockwise_sa.h: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:80,
from repeat_builder.cpp:26:
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 repeat_builder.cpp:31:
repeat_builder.cpp: In instantiation of ‘RepeatBuilder<TStr>::RepeatBuilder(TStr&, const EList<RefRecord>&, const EList<std::__cxx11::basic_string<char> >&, bool, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’:
repeat_builder.cpp:4753:16: required from here
repeat_builder.h:947:17: warning: ‘RepeatBuilder<SString<char> >::coordHelper_’ will be initialized after [-Wreorder]
947 | CoordHelper coordHelper_;
| ^~~~~~~~~~~~
repeat_builder.h:940:10: warning: ‘bool RepeatBuilder<SString<char> >::forward_only_’ [-Wreorder]
940 | bool forward_only_;
| ^~~~~~~~~~~~~
repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder]
3167 | RepeatBuilder<TStr>::RepeatBuilder(TStr& s,
| ^~~~~~~~~~~~~~~~~~~
repeat_builder.cpp: In instantiation of ‘void RepeatBuilder<TStr>::build(const RepeatParameter&) [with TStr = SString<char>]’:
repeat_builder.cpp:4753:16: required from here
repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
3396 | if(spos != string::npos) {
| ~~~~~^~~~~~~~~~~~~~~
repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
3426 | if(spos != string::npos) {
| ~~~~~^~~~~~~~~~~~~~~
repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
3553 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const unsigned int’} [-Wsign-compare]
3563 | if(pos != string::npos) {
| ~~~~^~~~~~~~~~~~~~~
repeat_builder.cpp: In instantiation of ‘void RepeatBuilder<TStr>::saveConsensus(const RepeatParameter&, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’:
repeat_builder.cpp:4753:16: required from here
repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘const int’ [-Wsign-compare]
4114 | if((oskip + out_len) == output_width) {
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString<char>]’:
repeat_builder.cpp:4754:46: required from here
repeat_builder.cpp:309:24: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare]
309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) {
| ~~~^~~~~~~~~~~~~~
repeat_builder.cpp:310:25: warning: array subscript has type ‘char’ [-Wchar-subscripts]
310 | buf.push_back("ACGTN"[s[i + j]]);
| ~~~~~~~^
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:80,
from repeat_builder.cpp:26:
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);
| ^~~~~~~~
repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long long unsigned int; size_t = unsigned int]’:
repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder<TStr>::build(const RepeatParameter&) [with TStr = SString<char>]’
repeat_builder.cpp:4753:16: required from here
repeat_builder.cpp:272:19: warning: array subscript has type ‘char’ [-Wchar-subscripts]
272 | char nt = "ACGT"[ref[start + i]];
| ~~~~~~^
repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString<char>; TIndexOffU = long long unsigned int; size_t = unsigned int; std::string = std::__cxx11::basic_string<char>]’:
repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder<TStr>::build(const RepeatParameter&) [with TStr = SString<char>]’
repeat_builder.cpp:4753:16: required from here
repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts]
286 | char nt = "ACGT"[ref[start + i]];
| ~~~~~~^
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:80,
from repeat_builder.cpp:26:
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
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-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-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-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-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-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: package could avoid a useless dependency if debian/hisat2/usr/bin/hisat2-align-l debian/hisat2/usr/bin/hisat2-build-l debian/hisat2/usr/bin/hisat2-inspect-s debian/hisat2/usr/bin/hisat2-align-s debian/hisat2/usr/bin/hisat2-build-s debian/hisat2/usr/bin/hisat2-inspect-l were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
debian/rules override_dh_gencontrol
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_gencontrol -- -Vsimde:Built-Using="simde (= 0.0.0.git.20200424-1), "
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'hisat2-dbgsym' in '../hisat2-dbgsym_2.2.0-2_armhf.deb'.
dpkg-deb: building package 'hisat2' in '../hisat2_2.2.0-2_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian 2019 test autobuilder <root@raspbian.org> >../hisat2_2.2.0-2_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 2020-05-09T05:38:10Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
hisat2_2.2.0-2_armhf.changes:
-----------------------------
Format: 1.8
Date: Wed, 06 May 2020 20:48:11 +0200
Source: hisat2
Binary: hisat2 hisat2-dbgsym
Architecture: armhf
Version: 2.2.0-2
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian 2019 test autobuilder <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 (2.2.0-2) unstable; urgency=medium
.
* Fix simde patch for ppc64el
* Fix missing $(LDFLAGS) in hardening patch
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Files:
f1c72a05f7153ae9a7ddfe0e77700b0e 10579472 debug optional hisat2-dbgsym_2.2.0-2_armhf.deb
d21e9a189dd8a8dedf9fa6c1c8b5c8d2 5239 science optional hisat2_2.2.0-2_armhf.buildinfo
d1d21ca44585aa65e2f0760880af9a50 3259080 science optional hisat2_2.2.0-2_armhf.deb
+------------------------------------------------------------------------------+
| Buildinfo |
+------------------------------------------------------------------------------+
Format: 1.0
Source: hisat2
Binary: hisat2 python3-hisat2
Architecture: armhf
Version: 2.2.0-2
Checksums-Md5:
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Checksums-Sha256:
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1a385bc726c97d0e09fbf24430f2327e259679e18485dd68237e7e79f487a45c 3259080 hisat2_2.2.0-2_armhf.deb
Build-Origin: Raspbian
Build-Architecture: armhf
Build-Date: Sat, 09 May 2020 05:38:07 +0000
Build-Path: /<<PKGBUILDDIR>>
Installed-Build-Depends:
autoconf (= 2.69-11.1),
automake (= 1:1.16.2-1),
autopoint (= 0.19.8.1-10),
autotools-dev (= 20180224.1),
base-files (= 11+rpi1),
base-passwd (= 3.5.47),
bash (= 5.0-6),
binutils (= 2.34-5+rpi1),
binutils-arm-linux-gnueabihf (= 2.34-5+rpi1),
binutils-common (= 2.34-5+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 (= 9.3.0-10+rpi1),
dash (= 0.5.10.2-7),
debconf (= 1.5.74),
debhelper (= 13),
debianutils (= 4.9.1),
dh-autoreconf (= 19),
dh-strip-nondeterminism (= 1.8.0-1),
diffutils (= 1:3.7-3),
dpkg (= 1.19.7),
dpkg-dev (= 1.19.7),
dwz (= 0.13-5),
fdisk (= 2.34-0.1),
file (= 1:5.38-4),
findutils (= 4.7.0-1),
g++ (= 4:9.2.1-3.1+rpi1),
g++-9 (= 9.3.0-10+rpi1),
gcc (= 4:9.2.1-3.1+rpi1),
gcc-10-base (= 10-20200418-1+rpi1),
gcc-9 (= 9.3.0-10+rpi1),
gcc-9-base (= 9.3.0-10+rpi1),
gettext (= 0.19.8.1-10),
gettext-base (= 0.19.8.1-10),
grep (= 3.4-1),
groff-base (= 1.22.4-4),
gzip (= 1.10-2),
help2man (= 1.47.15),
hostname (= 3.23),
init-system-helpers (= 1.57),
intltool-debian (= 0.35.0+20060710.5),
libacl1 (= 2.2.53-6),
libarchive-zip-perl (= 1.68-1),
libasan5 (= 9.3.0-10+rpi1),
libatomic1 (= 10-20200418-1+rpi1),
libattr1 (= 1:2.4.48-5),
libaudit-common (= 1:2.8.5-3),
libaudit1 (= 1:2.8.5-3),
libbinutils (= 2.34-5+rpi1),
libblkid1 (= 2.34-0.1),
libbsd0 (= 0.10.0-1),
libbz2-1.0 (= 1.0.8-2),
libc-bin (= 2.30-4+rpi1),
libc-dev-bin (= 2.30-4+rpi1),
libc6 (= 2.30-4+rpi1),
libc6-dev (= 2.30-4+rpi1),
libcap-ng0 (= 0.7.9-2.1+b1),
libcc1-0 (= 10-20200418-1+rpi1),
libcroco3 (= 0.6.13-1),
libcrypt-dev (= 1:4.4.16-1),
libcrypt1 (= 1:4.4.16-1),
libctf-nobfd0 (= 2.34-5+rpi1),
libctf0 (= 2.34-5+rpi1),
libdb5.3 (= 5.3.28+dfsg1-0.6),
libdebconfclient0 (= 0.251),
libdebhelper-perl (= 13),
libdpkg-perl (= 1.19.7),
libelf1 (= 0.176-1.1),
libexpat1 (= 2.2.9-1),
libfdisk1 (= 2.34-0.1),
libffi7 (= 3.3-4),
libfile-stripnondeterminism-perl (= 1.8.0-1),
libgcc-9-dev (= 9.3.0-10+rpi1),
libgcc-s1 (= 10-20200418-1+rpi1),
libgcc1 (= 1:10-20200418-1+rpi1),
libgcrypt20 (= 1.8.5-5),
libgdbm-compat4 (= 1.18.1-5),
libgdbm6 (= 1.18.1-5),
libglib2.0-0 (= 2.64.2-1),
libgmp10 (= 2:6.2.0+dfsg-4),
libgomp1 (= 10-20200418-1+rpi1),
libgpg-error0 (= 1.37-1),
libicu63 (= 63.2-3),
libisl22 (= 0.22.1-1),
liblocale-gettext-perl (= 1.07-4),
liblz4-1 (= 1.9.2-2),
liblzma5 (= 5.2.4-1),
libmagic-mgc (= 1:5.38-4),
libmagic1 (= 1:5.38-4),
libmount1 (= 2.34-0.1),
libmpc3 (= 1.1.0-1),
libmpdec2 (= 2.4.2-3),
libmpfr6 (= 4.0.2-1),
libncursesw6 (= 6.2-1),
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 (= 10.34-7),
libpcre3 (= 2:8.39-12),
libperl5.30 (= 5.30.0-10),
libpipeline1 (= 1.5.2-2),
libpython3-stdlib (= 3.8.2-3),
libpython3.8-minimal (= 3.8.3~rc1-1),
libpython3.8-stdlib (= 3.8.3~rc1-1),
libreadline8 (= 8.0-4),
libseccomp2 (= 2.4.3-1+rpi1),
libselinux1 (= 3.0-1+b1),
libsigsegv2 (= 2.12-2),
libsimde-dev (= 0.0.0.git.20200424-1),
libsmartcols1 (= 2.34-0.1),
libsqlite3-0 (= 3.31.1-5),
libssl1.1 (= 1.1.1g-1),
libstdc++-9-dev (= 9.3.0-10+rpi1),
libstdc++6 (= 10-20200418-1+rpi1),
libsub-override-perl (= 0.09-2),
libsystemd0 (= 245.5-1+rpi1),
libtinfo5 (= 6.2-1),
libtinfo6 (= 6.2-1),
libtool (= 2.4.6-14),
libubsan1 (= 10-20200418-1+rpi1),
libuchardet0 (= 0.0.6-3),
libudev1 (= 245.5-1+rpi1),
libunistring2 (= 0.9.10-2),
libuuid1 (= 2.34-0.1),
libxml2 (= 2.9.10+dfsg-5),
linux-libc-dev (= 5.2.17-1+rpi1+b2),
login (= 1:4.8.1-1),
lsb-base (= 11.1.0+rpi1),
m4 (= 1.4.18-4),
make (= 4.2.1-1.2),
man-db (= 2.9.1-1),
mawk (= 1.3.4.20200120-2),
mime-support (= 3.64),
ncurses-base (= 6.2-1),
ncurses-bin (= 6.2-1),
pandoc (= 2.5-3+b1),
pandoc-data (= 2.5-3),
patch (= 2.7.6-6),
perl (= 5.30.0-10),
perl-base (= 5.30.0-10),
perl-modules-5.30 (= 5.30.0-10),
po-debconf (= 1.0.21),
python3 (= 3.8.2-3),
python3-minimal (= 3.8.2-3),
python3.8 (= 3.8.3~rc1-1),
python3.8-minimal (= 3.8.3~rc1-1),
readline-common (= 8.0-4),
sed (= 4.7-1),
sensible-utils (= 0.0.12+nmu1),
sysvinit-utils (= 2.96-3),
tar (= 1.30+dfsg-7),
util-linux (= 2.34-0.1),
xz-utils (= 5.2.4-1),
zlib1g (= 1:1.2.11.dfsg-2)
Environment:
DEB_BUILD_OPTIONS="parallel=4"
LANG="en_GB.UTF-8"
LC_ALL="POSIX"
SOURCE_DATE_EPOCH="1588790891"
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
hisat2-dbgsym_2.2.0-2_armhf.deb
-------------------------------
new Debian package, version 2.0.
size 10579472 bytes: control archive=860 bytes.
573 bytes, 12 lines control
722 bytes, 7 lines md5sums
Package: hisat2-dbgsym
Source: hisat2
Version: 2.2.0-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 10834
Depends: hisat2 (= 2.2.0-2)
Section: debug
Priority: optional
Description: debug symbols for hisat2
Build-Ids: 10294b59ea2eb602d7b7108b7a61c25568a70b64 3c0afc51b0c135c56841ddc21b3825ee4380f68c 41ffb62a6f7b87e48e8ef3ecabdc20e2f2f08af5 4ec76d96473b6c1b86f76355da9960d6dc4c8a4e 8e4261cb31176c363ed14b25cc1538161e104baa fc38fde7a4ad9667f4115e6f53f319a3f0ac662a
drwxr-xr-x root/root 0 2020-05-06 18:48 ./
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.build-id/10/
-rw-r--r-- root/root 2873328 2020-05-06 18:48 ./usr/lib/debug/.build-id/10/294b59ea2eb602d7b7108b7a61c25568a70b64.debug
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.build-id/3c/
-rw-r--r-- root/root 2870192 2020-05-06 18:48 ./usr/lib/debug/.build-id/3c/0afc51b0c135c56841ddc21b3825ee4380f68c.debug
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.build-id/41/
-rw-r--r-- root/root 890068 2020-05-06 18:48 ./usr/lib/debug/.build-id/41/ffb62a6f7b87e48e8ef3ecabdc20e2f2f08af5.debug
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.build-id/4e/
-rw-r--r-- root/root 890328 2020-05-06 18:48 ./usr/lib/debug/.build-id/4e/c76d96473b6c1b86f76355da9960d6dc4c8a4e.debug
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.build-id/8e/
-rw-r--r-- root/root 1489548 2020-05-06 18:48 ./usr/lib/debug/.build-id/8e/4261cb31176c363ed14b25cc1538161e104baa.debug
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.build-id/fc/
-rw-r--r-- root/root 1485776 2020-05-06 18:48 ./usr/lib/debug/.build-id/fc/38fde7a4ad9667f4115e6f53f319a3f0ac662a.debug
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 574904 2020-05-06 18:48 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/hisat2.debug
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/share/
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-05-06 18:48 ./usr/share/doc/hisat2-dbgsym -> hisat2
hisat2_2.2.0-2_armhf.deb
------------------------
new Debian package, version 2.0.
size 3259080 bytes: control archive=1852 bytes.
1299 bytes, 23 lines control
2420 bytes, 33 lines md5sums
Package: hisat2
Version: 2.2.0-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 12747
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 9), perl:any, python3
Recommends: python3-hisat2, bcftools, samtools
Built-Using: simde (= 0.0.0.git.20200424-1)
Section: science
Priority: optional
Homepage: https://daehwankimlab.github.io/hisat2/
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).
drwxr-xr-x root/root 0 2020-05-06 18:48 ./
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/
drwxr-xr-x root/root 0 2020-05-06 18:48 ./usr/bin/
-rwxr-xr-x root/root 19653 2020-05-06 18:48 ./usr/bin/hisat2
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-rwxr-xr-x root/root 1554388 2020-05-06 18:48 ./usr/bin/hisat2-align-s
-rwxr-xr-x root/root 2804 2020-05-06 18:48 ./usr/bin/hisat2-build
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build Type: any
Build-Space: 115028
Build-Time: 1583
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 452
Job: hisat2_2.2.0-2
Machine Architecture: armhf
Package: hisat2
Package-Time: 2098
Source-Version: 2.2.0-2
Space: 115028
Status: successful
Version: 2.2.0-2
--------------------------------------------------------------------------------
Finished at 2020-05-09T05:38:10Z
Build needed 00:34:58, 115028k disk space