sbuild (Debian sbuild) 0.85.0 (04 January 2023) on mjolnir.einval.org

+==============================================================================+
| hisat2 2.2.1-4 (amd64)                       Mon, 29 Apr 2024 04:17:40 +0000 |
+==============================================================================+

Package: hisat2
Version: 2.2.1-4
Source Version: 2.2.1-4
Distribution: unstable
Machine Architecture: arm64
Host Architecture: amd64
Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any

Unpacking /home/helmut/.cache/sbuild/unstable-arm64-sbuild.tar.zst to /tmp/tmp.sbuild.EovkEBuofj...
I: NOTICE: Log filtering will replace 'sbuild-unshare-dummy-location' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/hisat2-tXaVL0/resolver-irlCLP' with '<<RESOLVERDIR>>'

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

Get:1 http://mirror.einval.org/debian unstable InRelease [198 kB]
Get:2 http://mirror.einval.org/debian unstable/main Sources [10.6 MB]
Get:3 http://mirror.einval.org/debian unstable/main arm64 Packages [9750 kB]
Get:4 http://mirror.einval.org/debian unstable/main amd64 Packages [9866 kB]
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Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages will be upgraded:
  libc-bin libc-dev-bin libc6 libc6-dev libperl5.38t64 perl perl-base
  perl-modules-5.38
8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 13.1 MB of archives.
After this operation, 3072 B disk space will be freed.
Get:1 http://mirror.einval.org/debian unstable/main arm64 libperl5.38t64 arm64 5.38.2-4 [4106 kB]
Get:2 http://mirror.einval.org/debian unstable/main arm64 perl arm64 5.38.2-4 [236 kB]
Get:3 http://mirror.einval.org/debian unstable/main arm64 perl-base arm64 5.38.2-4 [1509 kB]
Get:4 http://mirror.einval.org/debian unstable/main arm64 perl-modules-5.38 all 5.38.2-4 [2907 kB]
Get:5 http://mirror.einval.org/debian unstable/main arm64 libc6-dev arm64 2.37-19 [1433 kB]
Get:6 http://mirror.einval.org/debian unstable/main arm64 libc-dev-bin arm64 2.37-19 [47.0 kB]
Get:7 http://mirror.einval.org/debian unstable/main arm64 libc6 arm64 2.37-19 [2325 kB]
Get:8 http://mirror.einval.org/debian unstable/main arm64 libc-bin arm64 2.37-19 [527 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Unpacking libperl5.38t64:arm64 (5.38.2-4) over (5.38.2-3.2+b2) ...
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Unpacking perl (5.38.2-4) over (5.38.2-3.2+b2) ...
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Unpacking perl-base (5.38.2-4) over (5.38.2-3.2+b2) ...
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Unpacking libc-bin (2.37-19) over (2.37-18) ...
Setting up libc-bin (2.37-19) ...
Setting up perl-modules-5.38 (5.38.2-4) ...
Setting up libperl5.38t64:arm64 (5.38.2-4) ...
Setting up libc-dev-bin (2.37-19) ...
Setting up perl (5.38.2-4) ...
Setting up libc6-dev:arm64 (2.37-19) ...
Processing triggers for libc-bin (2.37-19) ...

+------------------------------------------------------------------------------+
| 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 6792 kB of source archives.
Get:1 http://mirror.einval.org/debian unstable/main hisat2 2.2.1-4 (dsc) [2129 B]
Get:2 http://mirror.einval.org/debian unstable/main hisat2 2.2.1-4 (tar) [6761 kB]
Get:3 http://mirror.einval.org/debian unstable/main hisat2 2.2.1-4 (diff) [29.1 kB]
Fetched 6792 kB in 0s (18.9 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hisat2-tXaVL0/hisat2-2.2.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hisat2-tXaVL0' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64
Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [609 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [786 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [802 B]
Fetched 2197 B in 0s (127 kB/s)
Reading package lists...
Reading package lists...

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

Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
Execute external solver...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu
  bsdextrautils cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config
  crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz fakeroot file g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu
  gcc-13-base:amd64 gcc-13-cross-base gcc-13-x86-64-linux-gnu
  gcc-13-x86-64-linux-gnu-base gcc-14-base:amd64 gcc-14-cross-base
  gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man
  intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross
  libatomic1:amd64 libatomic1-amd64-cross libc6:amd64 libc6-amd64-cross
  libc6-dev:amd64 libc6-dev-amd64-cross libconfig-auto-perl
  libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1t64 libexpat1 libfakeroot
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libgcc-13-dev:amd64 libgcc-13-dev-amd64-cross libgcc-s1:amd64
  libgcc-s1-amd64-cross libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64
  libhwasan0-amd64-cross libicu72 libio-string-perl libitm1:amd64
  libitm1-amd64-cross liblocale-gettext-perl liblsan0:amd64
  liblsan0-amd64-cross liblua5.4-0 libmagic-mgc libmagic1t64 libncursesw6
  libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib
  libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 libsimde-dev
  libsqlite3-0 libstdc++-13-dev:amd64 libstdc++-13-dev-amd64-cross
  libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtool
  libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-0-2
  libyaml-perl m4 man-db media-types netbase pandoc pandoc-data po-debconf
  python3 python3-minimal python3.11 python3.11-minimal readline-common
  sensible-utils tzdata ucf
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-13-locales
  cpp-13-doc cpp-doc dh-make binutils-multiarch gcc-13-doc manpages-dev flex
  bison gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev
  libgettextpo-dev groff glibc-doc:amd64 libc-l10n:amd64 locales:amd64
  libnss-nis:amd64 libnss-nisplus:amd64 manpages-dev:amd64
  libstdc++-13-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk
  libyaml-shell-perl 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 libjs-katex citation-style-language-styles
  libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv
  python3.11-doc binfmt-support readline-doc
Recommended packages:
  curl | wget | lynx libidn2-0:amd64 libarchive-cpio-perl libgpm2 libltdl-dev
  libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl
  libmail-sendmail-perl ca-certificates
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu
  bsdextrautils cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config
  crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz fakeroot file g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu
  gcc-13-base:amd64 gcc-13-cross-base gcc-13-x86-64-linux-gnu
  gcc-13-x86-64-linux-gnu-base gcc-14-base:amd64 gcc-14-cross-base
  gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man
  intltool-debian libarchive-zip-perl libasan8:amd64 libasan8-amd64-cross
  libatomic1:amd64 libatomic1-amd64-cross libc6:amd64 libc6-amd64-cross
  libc6-dev:amd64 libc6-dev-amd64-cross libconfig-auto-perl
  libconfig-inifiles-perl libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1t64 libexpat1 libfakeroot
  libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl
  libgcc-13-dev:amd64 libgcc-13-dev-amd64-cross libgcc-s1:amd64
  libgcc-s1-amd64-cross libgomp1:amd64 libgomp1-amd64-cross libhwasan0:amd64
  libhwasan0-amd64-cross libicu72 libio-string-perl libitm1:amd64
  libitm1-amd64-cross liblocale-gettext-perl liblsan0:amd64
  liblsan0-amd64-cross liblua5.4-0 libmagic-mgc libmagic1t64 libncursesw6
  libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib
  libquadmath0:amd64 libquadmath0-amd64-cross libreadline8t64 libsimde-dev
  libsqlite3-0 libstdc++-13-dev:amd64 libstdc++-13-dev-amd64-cross
  libstdc++6:amd64 libstdc++6-amd64-cross libsub-override-perl libtool
  libtsan2:amd64 libtsan2-amd64-cross libubsan1:amd64 libubsan1-amd64-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-0-2
  libyaml-perl m4 man-db media-types netbase pandoc pandoc-data po-debconf
  python3 python3-minimal python3.11 python3.11-minimal readline-common
  sbuild-build-depends-main-dummy:amd64 sensible-utils tzdata ucf
0 upgraded, 115 newly installed, 0 to remove and 0 not upgraded.
Need to get 129 MB of archives.
After this operation, 661 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B]
Get:2 http://mirror.einval.org/debian unstable/main arm64 liblocale-gettext-perl arm64 1.07-7 [14.8 kB]
Get:3 http://mirror.einval.org/debian unstable/main arm64 libpython3.11-minimal arm64 3.11.9-1 [813 kB]
Get:4 http://mirror.einval.org/debian unstable/main arm64 libexpat1 arm64 2.6.2-1 [88.7 kB]
Get:5 http://mirror.einval.org/debian unstable/main arm64 python3.11-minimal arm64 3.11.9-1 [1767 kB]
Get:6 http://mirror.einval.org/debian unstable/main arm64 python3-minimal arm64 3.11.8-1 [26.3 kB]
Get:7 http://mirror.einval.org/debian unstable/main arm64 media-types all 10.1.0 [26.9 kB]
Get:8 http://mirror.einval.org/debian unstable/main arm64 netbase all 6.4 [12.8 kB]
Get:9 http://mirror.einval.org/debian unstable/main arm64 tzdata all 2024a-3 [255 kB]
Get:10 http://mirror.einval.org/debian unstable/main arm64 libncursesw6 arm64 6.4+20240414-1 [124 kB]
Get:11 http://mirror.einval.org/debian unstable/main arm64 readline-common all 8.2-4 [69.3 kB]
Get:12 http://mirror.einval.org/debian unstable/main arm64 libreadline8t64 arm64 8.2-4 [157 kB]
Get:13 http://mirror.einval.org/debian unstable/main arm64 libsqlite3-0 arm64 3.45.3-1 [837 kB]
Get:14 http://mirror.einval.org/debian unstable/main arm64 libpython3.11-stdlib arm64 3.11.9-1 [1775 kB]
Get:15 http://mirror.einval.org/debian unstable/main arm64 python3.11 arm64 3.11.9-1 [602 kB]
Get:16 http://mirror.einval.org/debian unstable/main arm64 libpython3-stdlib arm64 3.11.8-1 [9332 B]
Get:17 http://mirror.einval.org/debian unstable/main arm64 python3 arm64 3.11.8-1 [27.4 kB]
Get:18 http://mirror.einval.org/debian unstable/main arm64 sensible-utils all 0.0.22 [22.4 kB]
Get:19 http://mirror.einval.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.45-3 [314 kB]
Get:20 http://mirror.einval.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.45-3 [100 kB]
Get:21 http://mirror.einval.org/debian unstable/main arm64 file arm64 1:5.45-3 [43.0 kB]
Get:22 http://mirror.einval.org/debian unstable/main arm64 gettext-base arm64 0.21-14+b1 [160 kB]
Get:23 http://mirror.einval.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b1 [69.0 kB]
Get:24 http://mirror.einval.org/debian unstable/main arm64 groff-base arm64 1.23.0-3+b1 [1126 kB]
Get:25 http://mirror.einval.org/debian unstable/main arm64 bsdextrautils arm64 2.40-8 [93.0 kB]
Get:26 http://mirror.einval.org/debian unstable/main arm64 libpipeline1 arm64 1.5.7-2 [36.5 kB]
Get:27 http://mirror.einval.org/debian unstable/main arm64 man-db arm64 2.12.1-1 [1394 kB]
Get:28 http://mirror.einval.org/debian unstable/main arm64 ucf all 3.0043+nmu1 [55.2 kB]
Get:29 http://mirror.einval.org/debian unstable/main arm64 m4 arm64 1.4.19-4 [277 kB]
Get:30 http://mirror.einval.org/debian unstable/main arm64 autoconf all 2.71-3 [332 kB]
Get:31 http://mirror.einval.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB]
Get:32 http://mirror.einval.org/debian unstable/main arm64 automake all 1:1.16.5-1.3 [823 kB]
Get:33 http://mirror.einval.org/debian unstable/main arm64 autopoint all 0.21-14 [496 kB]
Get:34 http://mirror.einval.org/debian unstable/main arm64 gcc-13-x86-64-linux-gnu-base arm64 13.2.0-12cross1 [42.6 kB]
Get:35 http://mirror.einval.org/debian unstable/main arm64 cpp-13-x86-64-linux-gnu arm64 13.2.0-12cross1 [9273 kB]
Get:36 http://mirror.einval.org/debian unstable/main arm64 cpp-x86-64-linux-gnu arm64 4:13.2.0-7 [4732 B]
Get:37 http://mirror.einval.org/debian unstable/main arm64 cross-config all 2.6.20 [16.3 kB]
Get:38 http://mirror.einval.org/debian unstable/main arm64 binutils-x86-64-linux-gnu arm64 2.42-4 [2376 kB]
Get:39 http://mirror.einval.org/debian unstable/main arm64 gcc-13-cross-base all 13.2.0-12cross1 [38.1 kB]
Get:40 http://mirror.einval.org/debian unstable/main arm64 gcc-14-cross-base all 14-20240127-1cross1 [37.9 kB]
Get:41 http://mirror.einval.org/debian unstable/main arm64 libgcc-s1-amd64-cross all 14-20240127-1cross1 [71.7 kB]
Get:42 http://mirror.einval.org/debian unstable/main arm64 libgomp1-amd64-cross all 14-20240127-1cross1 [128 kB]
Get:43 http://mirror.einval.org/debian unstable/main arm64 libitm1-amd64-cross all 14-20240127-1cross1 [25.2 kB]
Get:44 http://mirror.einval.org/debian unstable/main arm64 libatomic1-amd64-cross all 14-20240127-1cross1 [8996 B]
Get:45 http://mirror.einval.org/debian unstable/main arm64 libasan8-amd64-cross all 14-20240127-1cross1 [2716 kB]
Get:46 http://mirror.einval.org/debian unstable/main arm64 liblsan0-amd64-cross all 14-20240127-1cross1 [1199 kB]
Get:47 http://mirror.einval.org/debian unstable/main arm64 libtsan2-amd64-cross all 14-20240127-1cross1 [2444 kB]
Get:48 http://mirror.einval.org/debian unstable/main arm64 libc6-amd64-cross all 2.37-12cross1 [1478 kB]
Get:49 http://mirror.einval.org/debian unstable/main arm64 libstdc++6-amd64-cross all 14-20240127-1cross1 [667 kB]
Get:50 http://mirror.einval.org/debian unstable/main arm64 libubsan1-amd64-cross all 14-20240127-1cross1 [1070 kB]
Get:51 http://mirror.einval.org/debian unstable/main arm64 libhwasan0-amd64-cross all 14-20240127-1cross1 [1434 kB]
Get:52 http://mirror.einval.org/debian unstable/main arm64 libquadmath0-amd64-cross all 14-20240127-1cross1 [146 kB]
Get:53 http://mirror.einval.org/debian unstable/main arm64 libgcc-13-dev-amd64-cross all 13.2.0-12cross1 [2536 kB]
Get:54 http://mirror.einval.org/debian unstable/main arm64 gcc-13-x86-64-linux-gnu arm64 13.2.0-12cross1 [17.8 MB]
Get:55 http://mirror.einval.org/debian unstable/main arm64 gcc-x86-64-linux-gnu arm64 4:13.2.0-7 [1452 B]
Get:56 http://mirror.einval.org/debian unstable/main arm64 libc6-dev-amd64-cross all 2.37-12cross1 [1898 kB]
Get:57 http://mirror.einval.org/debian unstable/main arm64 libstdc++-13-dev-amd64-cross all 13.2.0-12cross1 [2210 kB]
Get:58 http://mirror.einval.org/debian unstable/main arm64 g++-13-x86-64-linux-gnu arm64 13.2.0-12cross1 [10.1 MB]
Get:59 http://mirror.einval.org/debian unstable/main arm64 g++-x86-64-linux-gnu arm64 4:13.2.0-7 [1204 B]
Get:60 http://mirror.einval.org/debian unstable/main arm64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB]
Get:61 http://mirror.einval.org/debian unstable/main arm64 libio-string-perl all 1.08-4 [12.1 kB]
Get:62 http://mirror.einval.org/debian unstable/main arm64 libicu72 arm64 72.1-4+b1 [9224 kB]
Get:63 http://mirror.einval.org/debian unstable/main arm64 libxml2 arm64 2.9.14+dfsg-1.3+b3 [624 kB]
Get:64 http://mirror.einval.org/debian unstable/main arm64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:65 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:66 http://mirror.einval.org/debian unstable/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:67 http://mirror.einval.org/debian unstable/main arm64 libxml-libxml-perl arm64 2.0207+dfsg+really+2.0134-1+b3 [299 kB]
Get:68 http://mirror.einval.org/debian unstable/main arm64 libxml-simple-perl all 2.25-2 [69.8 kB]
Get:69 http://mirror.einval.org/debian unstable/main arm64 libyaml-perl all 1.31-1 [64.8 kB]
Get:70 http://mirror.einval.org/debian unstable/main arm64 libconfig-auto-perl all 0.44-2 [19.2 kB]
Get:71 http://mirror.einval.org/debian unstable/main arm64 libfile-which-perl all 1.27-2 [15.1 kB]
Get:72 http://mirror.einval.org/debian unstable/main arm64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get:73 http://mirror.einval.org/debian unstable/main arm64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB]
Get:74 http://mirror.einval.org/debian unstable/main arm64 dpkg-cross all 2.6.20 [25.8 kB]
Get:75 http://mirror.einval.org/debian unstable/main arm64 crossbuild-essential-amd64 all 12.10 [3488 B]
Get:76 http://mirror.einval.org/debian unstable/main arm64 libdebhelper-perl all 13.15.3 [88.0 kB]
Get:77 http://mirror.einval.org/debian unstable/main arm64 libtool all 2.4.7-7 [517 kB]
Get:78 http://mirror.einval.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB]
Get:79 http://mirror.einval.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:80 http://mirror.einval.org/debian unstable/main arm64 libsub-override-perl all 0.10-1 [10.6 kB]
Get:81 http://mirror.einval.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:82 http://mirror.einval.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:83 http://mirror.einval.org/debian unstable/main arm64 libelf1t64 arm64 0.191-1+b1 [187 kB]
Get:84 http://mirror.einval.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB]
Get:85 http://mirror.einval.org/debian unstable/main arm64 gettext arm64 0.21-14+b1 [1249 kB]
Get:86 http://mirror.einval.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:87 http://mirror.einval.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:88 http://mirror.einval.org/debian unstable/main arm64 debhelper all 13.15.3 [901 kB]
Get:89 http://mirror.einval.org/debian unstable/main arm64 libfakeroot arm64 1.34-1 [28.4 kB]
Get:90 http://mirror.einval.org/debian unstable/main arm64 fakeroot arm64 1.34-1 [73.5 kB]
Get:91 http://mirror.einval.org/debian unstable/main amd64 gcc-13-base amd64 13.2.0-23 [44.6 kB]
Get:92 http://mirror.einval.org/debian unstable/main amd64 gcc-14-base amd64 14-20240330-1 [43.2 kB]
Get:93 http://mirror.einval.org/debian unstable/main arm64 help2man arm64 1.49.3 [198 kB]
Get:94 http://mirror.einval.org/debian unstable/main amd64 libgcc-s1 amd64 14-20240330-1 [71.9 kB]
Get:95 http://mirror.einval.org/debian unstable/main amd64 libc6 amd64 2.37-19 [2759 kB]
Get:96 http://mirror.einval.org/debian unstable/main amd64 libasan8 amd64 14-20240330-1 [2724 kB]
Get:97 http://mirror.einval.org/debian unstable/main amd64 libatomic1 amd64 14-20240330-1 [9216 B]
Get:98 http://mirror.einval.org/debian unstable/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB]
Get:99 http://mirror.einval.org/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB]
Get:100 http://mirror.einval.org/debian unstable/main amd64 libc6-dev amd64 2.37-19 [1906 kB]
Get:101 http://mirror.einval.org/debian unstable/main amd64 libgomp1 amd64 14-20240330-1 [136 kB]
Get:102 http://mirror.einval.org/debian unstable/main amd64 libitm1 amd64 14-20240330-1 [25.8 kB]
Get:103 http://mirror.einval.org/debian unstable/main amd64 liblsan0 amd64 14-20240330-1 [1201 kB]
Get:104 http://mirror.einval.org/debian unstable/main amd64 libtsan2 amd64 14-20240330-1 [2454 kB]
Get:105 http://mirror.einval.org/debian unstable/main amd64 libstdc++6 amd64 14-20240330-1 [713 kB]
Get:106 http://mirror.einval.org/debian unstable/main amd64 libubsan1 amd64 14-20240330-1 [1071 kB]
Get:107 http://mirror.einval.org/debian unstable/main amd64 libhwasan0 amd64 14-20240330-1 [1485 kB]
Get:108 http://mirror.einval.org/debian unstable/main amd64 libquadmath0 amd64 14-20240330-1 [147 kB]
Get:109 http://mirror.einval.org/debian unstable/main amd64 libgcc-13-dev amd64 13.2.0-23 [2537 kB]
Get:110 http://mirror.einval.org/debian unstable/main arm64 liblua5.4-0 arm64 5.4.6-3+b1 [135 kB]
Get:111 http://mirror.einval.org/debian unstable/main arm64 libsimde-dev all 0.8.0-1 [458 kB]
Get:112 http://mirror.einval.org/debian unstable/main amd64 libstdc++-13-dev amd64 13.2.0-23 [2264 kB]
Get:113 http://mirror.einval.org/debian unstable/main arm64 libyaml-0-2 arm64 0.2.5-1+b1 [49.0 kB]
Get:114 http://mirror.einval.org/debian unstable/main arm64 pandoc-data all 3.1.3-1 [445 kB]
Get:115 http://mirror.einval.org/debian unstable/main arm64 pandoc arm64 3.1.3+ds-3 [24.2 MB]
debconf: delaying package configuration, since apt-utils is not installed
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Current default time zone: 'Etc/UTC'
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update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
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+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in any all)

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

Kernel: Linux 6.1.0-7-arm64 #1 SMP Debian 6.1.20-1 (2023-03-19) arm64 (aarch64)
Toolchain package versions: binutils_2.42-4 dpkg-dev_1.22.6 g++-13_13.2.0-23 gcc-13_13.2.0-23 libc6-dev_2.37-19 libstdc++-13-dev_13.2.0-23 libstdc++-13-dev-amd64-cross_13.2.0-12cross1 libstdc++6_14-20240330-1 libstdc++6-amd64-cross_14-20240127-1cross1 linux-libc-dev_6.7.12-1
Package versions: apt_2.9.2 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-14 autotools-dev_20220109.1 base-files_13.1 base-passwd_3.6.3 bash_5.2.21-2 binutils_2.42-4 binutils-aarch64-linux-gnu_2.42-4 binutils-common_2.42-4 binutils-x86-64-linux-gnu_2.42-4 bsdextrautils_2.40-8 bsdutils_1:2.40-8 build-essential_12.10 bzip2_1.0.8-5.1 coreutils_9.4-3.1 cpp_4:13.2.0-7 cpp-13_13.2.0-23 cpp-13-aarch64-linux-gnu_13.2.0-23 cpp-13-x86-64-linux-gnu_13.2.0-12cross1 cpp-aarch64-linux-gnu_4:13.2.0-7 cpp-x86-64-linux-gnu_4:13.2.0-7 cross-config_2.6.20 crossbuild-essential-amd64_12.10 dash_0.5.12-6 debconf_1.5.86 debhelper_13.15.3 debian-archive-keyring_2023.4 debianutils_5.17 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.10-1 dpkg_1.22.6 dpkg-cross_2.6.20 dpkg-dev_1.22.6 dwz_0.15-1+b1 fakeroot_1.34-1 file_1:5.45-3 findutils_4.9.0-5 g++_4:13.2.0-7 g++-13_13.2.0-23 g++-13-aarch64-linux-gnu_13.2.0-23 g++-13-x86-64-linux-gnu_13.2.0-12cross1 g++-aarch64-linux-gnu_4:13.2.0-7 g++-x86-64-linux-gnu_4:13.2.0-7 gcc_4:13.2.0-7 gcc-13_13.2.0-23 gcc-13-aarch64-linux-gnu_13.2.0-23 gcc-13-base_13.2.0-23 gcc-13-cross-base_13.2.0-12cross1 gcc-13-x86-64-linux-gnu_13.2.0-12cross1 gcc-13-x86-64-linux-gnu-base_13.2.0-12cross1 gcc-14-base_14-20240330-1 gcc-14-cross-base_14-20240127-1cross1 gcc-aarch64-linux-gnu_4:13.2.0-7 gcc-x86-64-linux-gnu_4:13.2.0-7 gettext_0.21-14+b1 gettext-base_0.21-14+b1 gpgv_2.2.40-3 grep_3.11-4 groff-base_1.23.0-3+b1 gzip_1.12-1.1 help2man_1.49.3 hostname_3.23+nmu2 init-system-helpers_1.66 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-1 libapt-pkg6.0t64_2.9.2 libarchive-zip-perl_1.68-1 libasan8_14-20240330-1 libasan8-amd64-cross_14-20240127-1cross1 libatomic1_14-20240330-1 libatomic1-amd64-cross_14-20240127-1cross1 libattr1_1:2.5.2-1 libaudit-common_1:3.1.2-2.1 libaudit1_1:3.1.2-2.1 libbinutils_2.42-4 libblkid1_2.40-8 libbz2-1.0_1.0.8-5.1 libc-bin_2.37-19 libc-dev-bin_2.37-19 libc6_2.37-19 libc6-amd64-cross_2.37-12cross1 libc6-dev_2.37-19 libc6-dev-amd64-cross_2.37-12cross1 libcap-ng0_0.8.5-1 libcap2_1:2.66-5 libcc1-0_14-20240330-1 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.36-4 libcrypt1_1:4.4.36-4 libctf-nobfd0_2.42-4 libctf0_2.42-4 libdb5.3t64_5.3.28+dfsg2-7 libdebconfclient0_0.271+b3 libdebhelper-perl_13.15.3 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.22.6 libelf1t64_0.191-1+b1 libexpat1_2.6.2-1 libfakeroot_1.34-1 libffi8_3.4.6-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-13-dev_13.2.0-23 libgcc-13-dev-amd64-cross_13.2.0-12cross1 libgcc-s1_14-20240330-1 libgcc-s1-amd64-cross_14-20240127-1cross1 libgcrypt20_1.10.3-2+b1 libgdbm-compat4t64_1.23-5.1+b1 libgdbm6t64_1.23-5.1+b1 libgmp10_2:6.3.0+dfsg-2+b1 libgnutls30t64_3.8.5-2 libgomp1_14-20240330-1 libgomp1-amd64-cross_14-20240127-1cross1 libgpg-error0_1.47-3+b1 libgprofng0_2.42-4 libhogweed6t64_3.9.1-2.2 libhwasan0_14-20240330-1 libhwasan0-amd64-cross_14-20240127-1cross1 libicu72_72.1-4+b1 libidn2-0_2.3.7-2 libio-string-perl_1.08-4 libisl23_0.26-3+b2 libitm1_14-20240330-1 libitm1-amd64-cross_14-20240127-1cross1 libjansson4_2.14-2+b2 liblocale-gettext-perl_1.07-7 liblsan0_14-20240330-1 liblsan0-amd64-cross_14-20240127-1cross1 liblua5.4-0_5.4.6-3+b1 liblz4-1_1.9.4-2 liblzma5_5.6.1+really5.4.5-1 libmagic-mgc_1:5.45-3 libmagic1t64_1:5.45-3 libmd0_1.1.0-2 libmount1_2.40-8 libmpc3_1.3.1-1+b2 libmpfr6_4.2.1-1+b1 libncursesw6_6.4+20240414-1 libnettle8t64_3.9.1-2.2 libnumber-compare-perl_0.03-3 libp11-kit0_0.25.3-4 libpam-modules_1.5.3-7 libpam-modules-bin_1.5.3-7 libpam-runtime_1.5.3-7 libpam0g_1.5.3-7 libpcre2-8-0_10.42-4+b1 libperl5.38t64_5.38.2-4 libpipeline1_1.5.7-2 libpython3-stdlib_3.11.8-1 libpython3.11-minimal_3.11.9-1 libpython3.11-stdlib_3.11.9-1 libquadmath0_14-20240330-1 libquadmath0-amd64-cross_14-20240127-1cross1 libreadline8t64_8.2-4 libseccomp2_2.5.5-1 libselinux1_3.5-2+b2 libsframe1_2.42-4 libsimde-dev_0.8.0-1 libsmartcols1_2.40-8 libsqlite3-0_3.45.3-1 libssl3t64_3.2.1-3 libstdc++-13-dev_13.2.0-23 libstdc++-13-dev-amd64-cross_13.2.0-12cross1 libstdc++6_14-20240330-1 libstdc++6-amd64-cross_14-20240127-1cross1 libsub-override-perl_0.10-1 libsystemd0_255.5-1 libtasn1-6_4.19.0-3+b2 libtext-glob-perl_0.11-3 libtinfo6_6.4+20240414-1 libtool_2.4.7-7 libtsan2_14-20240330-1 libtsan2-amd64-cross_14-20240127-1cross1 libubsan1_14-20240330-1 libubsan1-amd64-cross_14-20240127-1cross1 libuchardet0_0.0.8-1+b1 libudev1_255.5-1 libunistring5_1.2-1 libuuid1_2.40-8 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b3 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.3+b3 libxxhash0_0.8.2-2+b1 libyaml-0-2_0.2.5-1+b1 libyaml-perl_1.31-1 libzstd1_1.5.5+dfsg2-2 linux-libc-dev_6.7.12-1 login_1:4.13+dfsg1-4 m4_1.4.19-4 make_4.3-4.1 man-db_2.12.1-1 mawk_1.3.4.20240123-1 media-types_10.1.0 ncurses-base_6.4+20240414-1 ncurses-bin_6.4+20240414-1 netbase_6.4 pandoc_3.1.3+ds-3 pandoc-data_3.1.3-1 patch_2.7.6-7 perl_5.38.2-4 perl-base_5.38.2-4 perl-modules-5.38_5.38.2-4 po-debconf_1.0.21+nmu1 python3_3.11.8-1 python3-minimal_3.11.8-1 python3.11_3.11.9-1 python3.11-minimal_3.11.9-1 readline-common_8.2-4 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.22 sysvinit-utils_3.09-1 tar_1.35+dfsg-3 tzdata_2024a-3 ucf_3.0043+nmu1 usrmerge_39 util-linux_2.40-8 xz-utils_5.6.1+really5.4.5-1 zlib1g_1:1.3.dfsg-3.1

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


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

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

Format: 3.0 (quilt)
Source: hisat2
Binary: hisat2, python3-hisat2
Architecture: any all
Version: 2.2.1-4
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Michael R. Crusoe <crusoe@debian.org>
Homepage: https://daehwankimlab.github.io/hisat2/
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/hisat2
Vcs-Git: https://salsa.debian.org/med-team/hisat2.git
Testsuite: autopkgtest
Testsuite-Triggers: bcftools, samtools
Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man <!nodoc>, pandoc <!nodoc>, python3:any <!nodoc>
Package-List:
 hisat2 deb science optional arch=any
 python3-hisat2 deb python optional arch=all
Checksums-Sha1:
 e09c36d93952eff1ebfd19545c38e173636bf662 6761242 hisat2_2.2.1.orig.tar.gz
 4f025a697c5a41a55a237309454a55fd214a57bf 29056 hisat2_2.2.1-4.debian.tar.xz
Checksums-Sha256:
 f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599 6761242 hisat2_2.2.1.orig.tar.gz
 b71212885b7b5445fcc60425eaa9fb22e1f1396f8a9241d6e430d0709d8c70b8 29056 hisat2_2.2.1-4.debian.tar.xz
Files:
 0d1fcfcaf7ba1e64eb68006bba5a3855 6761242 hisat2_2.2.1.orig.tar.gz
 85767e7119a42490cc50c90a3d16dc95 29056 hisat2_2.2.1-4.debian.tar.xz

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gpgv: Signature made Fri Oct 14 18:23:54 2022 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify inline signature for ./hisat2_2.2.1-4.dsc: no acceptable signature found
dpkg-source: info: extracting hisat2 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz
dpkg-source: info: unpacking hisat2_2.2.1-4.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
dpkg-source: info: applying riscv5

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

Sufficient free space for build

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

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64
DEB_BUILD_OPTIONS=nocheck
HOME=/var/lib/sbuild
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmut
OLDPWD=/
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
PWD=/<<PKGBUILDDIR>>
SHELL=/bin/sh
USER=helmut

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

Command: dpkg-buildpackage --sanitize-env -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package hisat2
dpkg-buildpackage: info: source version 2.2.1-4
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   dh_auto_clean
	make -j1 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="14 October 2022" all doc
	make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc BUILD_HOST=Debian "BUILD_TIME=14 October 2022" all doc
make[2]: Entering directory '/<<PKGBUILDDIR>>'
x86_64-linux-gnu-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="\"14 October 2022\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -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
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h: In instantiation of ‘void GFM<index_t>::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::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:1039:23:   required from ‘GFM<index_t>::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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:786:39:   required from here
gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable]
 2167 |                         index_t template_len = 0;
      |                                 ^~~~~~~~~~~~
In file included from sequence_io.h:30,
                 from hisat2_build.cpp:28:
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:685:15,
    inlined from ‘RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]’ at rfm.h:768:29:
sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  602 |                         delete cs_;
      |                         ^~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]’ at rfm.h:764:24:
sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’
  610 |                         cs_ = new T[sz+1];
      |                               ^~~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:685:15,
    inlined from ‘RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]’ at rfm.h:766:29:
sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  602 |                         delete cs_;
      |                         ^~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]’ at rfm.h:764:24:
sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’
  610 |                         cs_ = new T[sz+1];
      |                               ^~~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:685:15,
    inlined from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]’ at hgfm.h:2259:41:
sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  602 |                         delete cs_;
      |                         ^~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]’ at hgfm.h:2255:36:
sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’
  610 |                         cs_ = new T[sz+1];
      |                               ^~~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:685:15,
    inlined from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]’ at hgfm.h:2257:41:
sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  602 |                         delete cs_;
      |                         ^~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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]’ at hgfm.h:2255:36:
sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’
  610 |                         cs_ = new T[sz+1];
      |                               ^~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)’:
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |                 uint64_t origBufOff = bufOff;
      |                          ^~~~~~~~~~
reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |         bool binarySearched = false;
      |              ^~~~~~~~~~~~~~
x86_64-linux-gnu-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="\"14 October 2022\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -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
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h: In instantiation of ‘void GFM<index_t>::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::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 unsigned int; std::string = std::__cxx11::basic_string<char>; std::ofstream = std::basic_ofstream<char>; uint32_t = unsigned int]’:
gfm.h:1039:23:   required from ‘GFM<index_t>::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 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 std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = long unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:535:15:   required from ‘void driver(const std::string&, EList<std::__cxx11::basic_string<char> >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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:786:39:   required from here
gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable]
 2167 |                         index_t template_len = 0;
      |                                 ^~~~~~~~~~~~
In file included from sequence_io.h:30,
                 from hisat2_build.cpp:28:
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:685:15,
    inlined from ‘RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int]’ at rfm.h:768:29:
sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  602 |                         delete cs_;
      |                         ^~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int]’ at rfm.h:764:24:
sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’
  610 |                         cs_ = new T[sz+1];
      |                               ^~~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:685:15,
    inlined from ‘RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int]’ at rfm.h:766:29:
sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  602 |                         delete cs_;
      |                         ^~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘RFM<index_t>::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int]’ at rfm.h:764:24:
sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’
  610 |                         cs_ = new T[sz+1];
      |                               ^~~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:685:15,
    inlined from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41:
sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  602 |                         delete cs_;
      |                         ^~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36:
sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’
  610 |                         cs_ = new T[sz+1];
      |                               ^~~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:687:9,
    inlined from ‘void SString<T>::install(const T*, size_t) [with T = char]’ at sstring.h:685:15,
    inlined from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41:
sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete]
  602 |                         delete cs_;
      |                         ^~~~~~~~~~
In member function ‘void SString<T>::resize(size_t) [with T = char]’,
    inlined from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::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 unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36:
sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’
  610 |                         cs_ = new T[sz+1];
      |                               ^~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)’:
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |                 uint64_t origBufOff = bufOff;
      |                          ^~~~~~~~~~
reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |         bool binarySearched = false;
      |              ^~~~~~~~~~~~~~
x86_64-linux-gnu-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="\"14 October 2022\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -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
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1823:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1823 |         auto_ptr<Presets> presets(new PresetsV0());
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3167:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3167 |         auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3168:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3168 |         auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3189:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3189 |         auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’:
hisat2.cpp:4035:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 4035 |         auto_ptr<BitPairReference> refs(
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
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>::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:3537:48:   required from here
hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare]
 5688 |                         if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off())
      |                                                                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
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 std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2.cpp:4351:26:   required from here
gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
 6935 |         int lastorig = -1;
      |             ^~~~~~~~
In file included from aligner_seed2.h:109,
                 from aligner_driver.h:78,
                 from hi_aligner.h:41:
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:1517:14:   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:5901:34:   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:3537:48:   required from here
group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 1224 |                                 for(index_t j = 0; j + 1 < st.back().map_.size(); j++) {
      |                                                    ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
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:3537:48:   required from here
hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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) {
      |                        ~~~~~~~~~~~^~~~~~~~~~~~~~
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:494:14:   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:1453:18:   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:5896:20:   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:3537:48:   required from here
group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  801 |                 if(new_bot - top < tmp_gbwt_to_node.size()) {
      |                    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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:3537:48:   required from here
hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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) {
      |                        ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
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 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;
      |                  ^~~~~~~~~~~~~~~
hi_aligner.h: In instantiation of ‘bool GenomeHit<index_t>::combineWith(const GenomeHit<index_t>&, const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long int]’:
spliced_aligner.h:494:60:   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 = unsigned int; local_index_t = short unsigned int; int64_t = long int]’
spliced_aligner.h:331:9:   required from here
hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long unsigned int’} and ‘char’ [-Wsign-compare]
 1926 |                     if(alt.seq == rdc) {
      |                        ~~~~~~~~^~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)’:
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |                 uint64_t origBufOff = bufOff;
      |                          ^~~~~~~~~~
reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |         bool binarySearched = false;
      |              ^~~~~~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from splice_site.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:
ds.h: In instantiation of ‘void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’:
splice_site.cpp:722:31:   required from here
ds.h:663:28: 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);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
splice_site.h:377:7: note: ‘class Exon’ declared here
  377 | class Exon {
      |       ^~~~
x86_64-linux-gnu-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="\"14 October 2022\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -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 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1823:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1823 |         auto_ptr<Presets> presets(new PresetsV0());
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3167:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3167 |         auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3168:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3168 |         auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3189:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 3189 |         auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’:
hisat2.cpp:4035:9: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 4035 |         auto_ptr<BitPairReference> refs(
      |         ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
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 unsigned int; local_index_t = short unsigned int]’:
hisat2.cpp:3537:48:   required from here
hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘TRefId’ {aka ‘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 unsigned int’ and ‘TRefOff’ {aka ‘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 int’} and ‘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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const 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 unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
 4614 |                         if(sink.numBestUnp(rdi).first > rp.khits) {
      |                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~
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 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 unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3537:48:   required from here
hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘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 unsigned int’ and ‘TRefOff’ {aka ‘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 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 unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3537:48:   required from here
hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
 5661 |             if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) {
      |                            ~~~~~^~~~~~~~~~~~
hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare]
 5688 |                         if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off())
      |                                                                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
gfm.h: In instantiation of ‘void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = long unsigned int]’:
hisat2.cpp:3815:17:   required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2.cpp:4351:26:   required from here
gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
 6935 |         int lastorig = -1;
      |             ^~~~~~~~
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 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 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 unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3537:48:   required from here
hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘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 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 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 unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3537:48:   required from here
hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘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 aligner_seed2.h:109,
                 from aligner_driver.h:78,
                 from hi_aligner.h:41:
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:1517:14:   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:5901:34:   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 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 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 unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3537:48:   required from here
group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 1224 |                                 for(index_t j = 0; j + 1 < st.back().map_.size(); j++) {
      |                                                    ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
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 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 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 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 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 unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3537:48:   required from here
hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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 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 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 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 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 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 unsigned int’ [-Wsign-compare]
 3454 |                     if(best_rdoff < rdoff + rd_i) {
      |                        ~~~~~~~~~~~^~~~~~~~~~~~~~
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:494:14:   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:1453:18:   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:5896:20:   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 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 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 unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3537:48:   required from here
group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 ‘long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
  801 |                 if(new_bot - top < tmp_gbwt_to_node.size()) {
      |                    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
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 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 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 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 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 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 unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3537:48:   required from here
hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long 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 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 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 ‘long 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 unsigned int’ and ‘int’ [-Wsign-compare]
 2744 |                     if(ht_list[h].first == ht_range.second) {
      |                        ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
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 unsigned int; local_index_t = short unsigned int; int64_t = 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 unsigned int’ and ‘int64_t’ {aka ‘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 unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare]
 1465 |                        combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) {
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
hi_aligner.h: In instantiation of ‘bool GenomeHit<index_t>::combineWith(const GenomeHit<index_t>&, const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long unsigned int; TAlScore = long int]’:
spliced_aligner.h:494:60:   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 unsigned int; local_index_t = short unsigned int; int64_t = long int]’
spliced_aligner.h:331:9:   required from here
hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long unsigned int’} and ‘char’ [-Wsign-compare]
 1926 |                     if(alt.seq == rdc) {
      |                        ~~~~~~~~^~~~~~
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 unsigned int; local_index_t = short unsigned int]’:
spliced_aligner.h:1086:53:   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 unsigned int; local_index_t = short unsigned int; int64_t = long int]’
spliced_aligner.h:331:9:   required from here
hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
 6719 |     if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) {
      |                                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)’:
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |                 uint64_t origBufOff = bufOff;
      |                          ^~~~~~~~~~
reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |         bool binarySearched = false;
      |              ^~~~~~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from splice_site.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM<long unsigned int>&, const EList<ALT<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 edit.h:29:
ds.h: In instantiation of ‘void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’:
splice_site.cpp:722:31:   required from here
ds.h:663:28: 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);
      |                 ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
splice_site.h:377:7: note: ‘class Exon’ declared here
  377 | class Exon {
      |       ^~~~
x86_64-linux-gnu-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="\"14 October 2022\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -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:227:18: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)’:
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
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:227:18: 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:
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
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:227:18: 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);
      |             ^~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
x86_64-linux-gnu-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="\"14 October 2022\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -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 hisat2_inspect.cpp:25:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:18: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)’:
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
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:227:18: 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:
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
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:227:18: 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);
      |             ^~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
x86_64-linux-gnu-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="\"14 October 2022\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -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
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadSizes(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’:
ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  367 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
ref_read.cpp: In function ‘std::pair<long unsigned int, long unsigned int> fastaRefReadFragsNames(EList<FileBuf*>&, EList<RefRecord>&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList<std::__cxx11::basic_string<char> >&)’:
ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  440 |             if(i + 1 >= recs.size() || recs[i+1].first) {
      |                ~~~~~~^~~~~~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |                 uint64_t origBufOff = bufOff;
      |                          ^~~~~~~~~~
reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |         bool binarySearched = false;
      |              ^~~~~~~~~~~~~~
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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   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:75,
                 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1185 |                 auto_ptr<stringstream> ss(new stringstream());
      |                 ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
gfm.h:1189:17: warning: ‘template<class> class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
 1189 |                 auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |                 ^~~~~~~~
/usr/x86_64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
repeat_builder.cpp: In function ‘std::string reverse_complement(const std::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 std::string&)’:
repeat_builder.cpp:200:53: 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 ‘long 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 std::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 std::string&, const std::string&, EList<long unsigned int>&, EList<long 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 ‘long 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 ‘long unsigned int’} [-Wsign-compare]
 1277 |         if(i == seq_len - 1) ed2[i] = add;
      |            ~~^~~~~~~~~~~~~~
repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::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 ‘long 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 std::string&, const std::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 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 std::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 std::__cxx11::basic_string<char>::size_type’ {aka ‘const long 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 std::__cxx11::basic_string<char>::size_type’ {aka ‘const long 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 std::__cxx11::basic_string<char>::size_type’ {aka ‘const long 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 std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
 3563 |                 if(pos != string::npos) {
      |                    ~~~~^~~~~~~~~~~~~~~
repeat_builder.cpp: In instantiation of ‘void RepeatBuilder<TStr>::saveConsensus(const RepeatParameter&, const std::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 ‘long 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:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  309 |                 for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) {
      |                                   ~~~^~~~~~~~~~~~~~
repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  310 |                         buf.push_back("ACGTN"[s[i + j]]);
      |                                       ~~~~~~~^
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 unsigned int; size_t = long 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:272:33: 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 unsigned int; size_t = long 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 /usr/x86_64-linux-gnu/include/c++/13/iostream:41,
                 from repeat_builder.cpp:21:
In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits<char>]’,
    inlined from ‘void RepeatBuilder<TStr>::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList<SeedExt>&, std::ostream&) [with TStr = SString<char>]’ at repeat_builder.cpp:3678:31:
/usr/x86_64-linux-gnu/include/c++/13/ostream:173:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized]
  173 |       { return _M_insert(__n); }
      |                ~~~~~~~~~^~~~~
repeat_builder.cpp: In member function ‘void RepeatBuilder<TStr>::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList<SeedExt>&, std::ostream&) [with TStr = SString<char>]’:
repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here
 3664 |         TIndexOffU pos_in_chr;
      |                    ^~~~~~~~~~
make[2]: Nothing to be done for 'doc'.
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: can't get `--help' info from ./hisat2
Try `--no-discard-stderr' if option outputs to stderr
make[1]: *** [debian/rules:32: override_dh_auto_build] Error 126
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:27: binary-arch] Error 2
dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2024-04-29T04:50:45Z

Finished
--------


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

Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)

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

Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 75276
Build-Time: 1879
Distribution: unstable
Fail-Stage: build
Foreign Architectures: amd64
Host Architecture: amd64
Install-Time: 63
Job: hisat2_2.2.1-4
Machine Architecture: arm64
Package: hisat2
Package-Time: 1985
Source-Version: 2.2.1-4
Space: 75276
Status: attempted
Version: 2.2.1-4
--------------------------------------------------------------------------------
Finished at 2024-04-29T04:50:45Z
Build needed 00:33:05, 75276k disk space