sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley

+==============================================================================+
| hisat2 2.2.1-4 (arm64)                       Tue, 12 Sep 2023 12:27:28 +0000 |
+==============================================================================+

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

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-880fae83-75a9-4cdf-9548-c9c117816f14' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/hisat2-vEMgBJ/resolver-fIz6HI' with '<<RESOLVERDIR>>'

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

Get:1 http://localhost:3142/debian sid InRelease [195 kB]
Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB]
Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB]
Get:4 http://localhost:3142/debian sid/main Sources T-2023-09-12-0824.31-F-2023-09-12-0203.08.pdiff [28.3 kB]
Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-09-12-0824.31-F-2023-09-12-0203.08.pdiff [13.3 kB]
Get:4 http://localhost:3142/debian sid/main Sources T-2023-09-12-0824.31-F-2023-09-12-0203.08.pdiff [28.3 kB]
Get:6 http://localhost:3142/debian sid/main arm64 Packages [9451 kB]
Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-09-12-0824.31-F-2023-09-12-0203.08.pdiff [13.3 kB]
Fetched 9815 kB in 3s (3571 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

+------------------------------------------------------------------------------+
| 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://localhost:3142/debian sid/main hisat2 2.2.1-4 (dsc) [2129 B]
Get:2 http://localhost:3142/debian sid/main hisat2 2.2.1-4 (tar) [6761 kB]
Get:3 http://localhost:3142/debian sid/main hisat2 2.2.1-4 (diff) [29.1 kB]
Fetched 6792 kB in 2s (3660 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hisat2-vEMgBJ/hisat2-2.2.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hisat2-vEMgBJ' 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:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64
Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64
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 (0 B/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-aarch64-linux-gnu
  bsdextrautils cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config
  crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu
  gcc-11-base:arm64 gcc-13-aarch64-linux-gnu gcc-13-aarch64-linux-gnu-base
  gcc-13-base:arm64 gcc-13-cross-base gcc-aarch64-linux-gnu gettext
  gettext-base groff-base help2man intltool-debian libarchive-zip-perl
  libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross
  libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross
  libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl
  libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:arm64
  libgcc-13-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross
  libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhwasan0:arm64
  libhwasan0-arm64-cross libicu72 libio-string-perl libitm1:arm64
  libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64
  libkrb5support0:arm64 liblocale-gettext-perl liblsan0:arm64
  liblsan0-arm64-cross liblua5.3-0 libmagic-mgc libmagic1 libncursesw6
  libnsl-dev:arm64 libnsl2:arm64 libpipeline1 libpython3-stdlib
  libpython3.11-minimal libpython3.11-stdlib libreadline8 libsimde-dev
  libsqlite3-0 libssl3:arm64 libstdc++-11-dev:arm64
  libstdc++-13-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross
  libsub-override-perl libtirpc-dev:arm64 libtirpc3:arm64 libtool
  libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-0-2
  libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db
  media-types pandoc pandoc-data po-debconf python3 python3-minimal python3.11
  python3.11-minimal readline-common sensible-utils 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-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev
  libgettextpo-dev groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64
  libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 krb5-doc:arm64
  krb5-user:arm64 libstdc++-11-doc:arm64 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:arm64 libarchive-cpio-perl krb5-locales:arm64
  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-aarch64-linux-gnu
  bsdextrautils cpp-13-aarch64-linux-gnu cpp-aarch64-linux-gnu cross-config
  crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-13-aarch64-linux-gnu g++-aarch64-linux-gnu
  gcc-11-base:arm64 gcc-13-aarch64-linux-gnu gcc-13-aarch64-linux-gnu-base
  gcc-13-base:arm64 gcc-13-cross-base gcc-aarch64-linux-gnu gettext
  gettext-base groff-base help2man intltool-debian libarchive-zip-perl
  libasan6:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross
  libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross
  libcom-err2:arm64 libconfig-auto-perl libconfig-inifiles-perl
  libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:arm64
  libgcc-13-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross
  libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2:arm64 libhwasan0:arm64
  libhwasan0-arm64-cross libicu72 libio-string-perl libitm1:arm64
  libitm1-arm64-cross libk5crypto3:arm64 libkeyutils1:arm64 libkrb5-3:arm64
  libkrb5support0:arm64 liblocale-gettext-perl liblsan0:arm64
  liblsan0-arm64-cross liblua5.3-0 libmagic-mgc libmagic1 libncursesw6
  libnsl-dev:arm64 libnsl2:arm64 libpipeline1 libpython3-stdlib
  libpython3.11-minimal libpython3.11-stdlib libreadline8 libsimde-dev
  libsqlite3-0 libssl3:arm64 libstdc++-11-dev:arm64
  libstdc++-13-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross
  libsub-override-perl libtirpc-dev:arm64 libtirpc3:arm64 libtool
  libtsan0:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-0-2
  libyaml-perl linux-libc-dev:arm64 linux-libc-dev-arm64-cross m4 man-db
  media-types pandoc pandoc-data po-debconf python3 python3-minimal python3.11
  python3.11-minimal readline-common sbuild-build-depends-main-dummy:arm64
  sensible-utils ucf
0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded.
Need to get 129 MB of archives.
After this operation, 620 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B]
Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-6 [15.3 kB]
Get:3 http://localhost:3142/debian sid/main amd64 libpython3.11-minimal amd64 3.11.5-3 [815 kB]
Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-2 [99.0 kB]
Get:5 http://localhost:3142/debian sid/main amd64 python3.11-minimal amd64 3.11.5-3 [2034 kB]
Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.11.4-5+b1 [26.5 kB]
Get:7 http://localhost:3142/debian sid/main amd64 media-types all 10.1.0 [26.9 kB]
Get:8 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.4+20230625-2 [134 kB]
Get:9 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.3 [69.0 kB]
Get:10 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.3 [166 kB]
Get:11 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.43.0-1 [870 kB]
Get:12 http://localhost:3142/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.5-3 [1802 kB]
Get:13 http://localhost:3142/debian sid/main amd64 python3.11 amd64 3.11.5-3 [582 kB]
Get:14 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.11.4-5+b1 [9492 B]
Get:15 http://localhost:3142/debian sid/main amd64 python3 amd64 3.11.4-5+b1 [26.5 kB]
Get:16 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB]
Get:17 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.45-2 [314 kB]
Get:18 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.45-2 [105 kB]
Get:19 http://localhost:3142/debian sid/main amd64 file amd64 1:5.45-2 [42.8 kB]
Get:20 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-13+b1 [161 kB]
Get:21 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB]
Get:22 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.23.0-2 [1176 kB]
Get:23 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.39.2-1 [88.7 kB]
Get:24 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB]
Get:25 http://localhost:3142/debian sid/main amd64 man-db amd64 2.11.2-3 [1386 kB]
Get:26 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB]
Get:27 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-4 [287 kB]
Get:28 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB]
Get:29 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB]
Get:30 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB]
Get:31 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-13 [496 kB]
Get:32 http://localhost:3142/debian sid/main amd64 binutils-aarch64-linux-gnu amd64 2.41-5 [3382 kB]
Get:33 http://localhost:3142/debian sid/main amd64 gcc-13-aarch64-linux-gnu-base amd64 13.2.0-2cross1 [39.6 kB]
Get:34 http://localhost:3142/debian sid/main amd64 cpp-13-aarch64-linux-gnu amd64 13.2.0-2cross1 [9758 kB]
Get:35 http://localhost:3142/debian sid/main amd64 cpp-aarch64-linux-gnu amd64 4:13.2.0-1 [4120 B]
Get:36 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB]
Get:37 http://localhost:3142/debian sid/main amd64 gcc-13-cross-base all 13.2.0-2cross1 [35.2 kB]
Get:38 http://localhost:3142/debian sid/main amd64 libc6-arm64-cross all 2.37-3cross1 [1002 kB]
Get:39 http://localhost:3142/debian sid/main amd64 libgcc-s1-arm64-cross all 13.2.0-2cross1 [40.9 kB]
Get:40 http://localhost:3142/debian sid/main amd64 libgomp1-arm64-cross all 13.2.0-2cross1 [112 kB]
Get:41 http://localhost:3142/debian sid/main amd64 libitm1-arm64-cross all 13.2.0-2cross1 [23.3 kB]
Get:42 http://localhost:3142/debian sid/main amd64 libatomic1-arm64-cross all 13.2.0-2cross1 [9876 B]
Get:43 http://localhost:3142/debian sid/main amd64 libasan8-arm64-cross all 13.2.0-2cross1 [2407 kB]
Get:44 http://localhost:3142/debian sid/main amd64 liblsan0-arm64-cross all 13.2.0-2cross1 [1068 kB]
Get:45 http://localhost:3142/debian sid/main amd64 libtsan2-arm64-cross all 13.2.0-2cross1 [2279 kB]
Get:46 http://localhost:3142/debian sid/main amd64 libstdc++6-arm64-cross all 13.2.0-2cross1 [575 kB]
Get:47 http://localhost:3142/debian sid/main amd64 libubsan1-arm64-cross all 13.2.0-2cross1 [980 kB]
Get:48 http://localhost:3142/debian sid/main amd64 libhwasan0-arm64-cross all 13.2.0-2cross1 [1119 kB]
Get:49 http://localhost:3142/debian sid/main amd64 libgcc-13-dev-arm64-cross all 13.2.0-2cross1 [2232 kB]
Get:50 http://localhost:3142/debian sid/main amd64 gcc-13-aarch64-linux-gnu amd64 13.2.0-2cross1 [19.2 MB]
Get:51 http://localhost:3142/debian sid/main amd64 gcc-aarch64-linux-gnu amd64 4:13.2.0-1 [1468 B]
Get:52 http://localhost:3142/debian sid/main amd64 linux-libc-dev-arm64-cross all 6.3.7-1cross1 [1894 kB]
Get:53 http://localhost:3142/debian sid/main amd64 libc6-dev-arm64-cross all 2.37-3cross1 [1424 kB]
Get:54 http://localhost:3142/debian sid/main amd64 libstdc++-13-dev-arm64-cross all 13.2.0-2cross1 [2132 kB]
Get:55 http://localhost:3142/debian sid/main amd64 g++-13-aarch64-linux-gnu amd64 13.2.0-2cross1 [10.7 MB]
Get:56 http://localhost:3142/debian sid/main amd64 g++-aarch64-linux-gnu amd64 4:13.2.0-1 [1172 B]
Get:57 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB]
Get:58 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB]
Get:59 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-3 [9376 kB]
Get:60 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [686 kB]
Get:61 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB]
Get:62 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB]
Get:63 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:64 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB]
Get:65 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB]
Get:66 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB]
Get:67 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB]
Get:68 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB]
Get:69 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB]
Get:70 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB]
Get:71 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB]
Get:72 http://localhost:3142/debian sid/main amd64 crossbuild-essential-arm64 all 12.10 [3484 B]
Get:73 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.6 [81.9 kB]
Get:74 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-7 [517 kB]
Get:75 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB]
Get:76 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB]
Get:77 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B]
Get:78 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB]
Get:79 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B]
Get:80 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.189-4 [174 kB]
Get:81 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB]
Get:82 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-13+b1 [1301 kB]
Get:83 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB]
Get:84 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB]
Get:85 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.6 [952 kB]
Get:86 http://localhost:3142/debian sid/main arm64 gcc-11-base arm64 11.4.0-3 [39.5 kB]
Get:87 http://localhost:3142/debian sid/main arm64 gcc-13-base arm64 13.2.0-3 [39.7 kB]
Get:88 http://localhost:3142/debian sid/main amd64 help2man amd64 1.49.3 [198 kB]
Get:89 http://localhost:3142/debian sid/main arm64 libgcc-s1 arm64 13.2.0-3 [40.8 kB]
Get:90 http://localhost:3142/debian sid/main arm64 libc6 arm64 2.37-8 [2320 kB]
Get:91 http://localhost:3142/debian sid/main arm64 libasan6 arm64 11.4.0-3 [1951 kB]
Get:92 http://localhost:3142/debian sid/main arm64 libatomic1 arm64 13.2.0-3 [10.2 kB]
Get:93 http://localhost:3142/debian sid/main arm64 linux-libc-dev arm64 6.4.13-1 [1806 kB]
Get:94 http://localhost:3142/debian sid/main arm64 libcrypt1 arm64 1:4.4.36-2 [90.3 kB]
Get:95 http://localhost:3142/debian sid/main arm64 libcrypt-dev arm64 1:4.4.36-2 [121 kB]
Get:96 http://localhost:3142/debian sid/main arm64 libcom-err2 arm64 1.47.0-2+b1 [19.9 kB]
Get:97 http://localhost:3142/debian sid/main arm64 libkrb5support0 arm64 1.20.1-3 [31.7 kB]
Get:98 http://localhost:3142/debian sid/main arm64 libk5crypto3 arm64 1.20.1-3 [79.2 kB]
Get:99 http://localhost:3142/debian sid/main arm64 libkeyutils1 arm64 1.6.3-2 [8844 B]
Get:100 http://localhost:3142/debian sid/main arm64 libssl3 arm64 3.0.10-1 [1801 kB]
Get:101 http://localhost:3142/debian sid/main arm64 libkrb5-3 arm64 1.20.1-3 [314 kB]
Get:102 http://localhost:3142/debian sid/main arm64 libgssapi-krb5-2 arm64 1.20.1-3 [123 kB]
Get:103 http://localhost:3142/debian sid/main arm64 libtirpc3 arm64 1.3.3+ds-1 [80.9 kB]
Get:104 http://localhost:3142/debian sid/main arm64 libnsl2 arm64 1.3.0-2 [36.9 kB]
Get:105 http://localhost:3142/debian sid/main arm64 libtirpc-dev arm64 1.3.3+ds-1 [194 kB]
Get:106 http://localhost:3142/debian sid/main arm64 libnsl-dev arm64 1.3.0-2 [66.1 kB]
Get:107 http://localhost:3142/debian sid/main arm64 libc6-dev arm64 2.37-8 [1428 kB]
Get:108 http://localhost:3142/debian sid/main arm64 libgomp1 arm64 13.2.0-3 [114 kB]
Get:109 http://localhost:3142/debian sid/main arm64 libitm1 arm64 13.2.0-3 [23.8 kB]
Get:110 http://localhost:3142/debian sid/main arm64 liblsan0 arm64 13.2.0-3 [1069 kB]
Get:111 http://localhost:3142/debian sid/main arm64 libtsan0 arm64 11.4.0-3 [1957 kB]
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Get:113 http://localhost:3142/debian sid/main arm64 libubsan1 arm64 13.2.0-3 [980 kB]
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Get:115 http://localhost:3142/debian sid/main arm64 libgcc-11-dev arm64 11.4.0-3 [931 kB]
Get:116 http://localhost:3142/debian sid/main amd64 liblua5.3-0 amd64 5.3.6-2 [123 kB]
Get:117 http://localhost:3142/debian sid/main amd64 libsimde-dev all 0.7.6-1 [384 kB]
Get:118 http://localhost:3142/debian sid/main arm64 libstdc++-11-dev arm64 11.4.0-3 [1935 kB]
Get:119 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB]
Get:120 http://localhost:3142/debian sid/main amd64 pandoc-data all 2.17.1.1-3 [418 kB]
Get:121 http://localhost:3142/debian sid/main amd64 pandoc amd64 2.17.1.1-3 [21.3 MB]
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update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
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update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10...
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Setting up libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+b1) ...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50...
update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50...
update-perl-sax-parsers: Updating overall Perl SAX parser modules info file...
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Setting up libgcc-s1:arm64 (13.2.0-3) ...
Setting up libc6:arm64 (2.37-8) ...
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Setting up libstdc++6:arm64 (13.2.0-3) ...
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Setting up libitm1:arm64 (13.2.0-3) ...
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Setting up libkeyutils1:arm64 (1.6.3-2) ...
Setting up libssl3:arm64 (3.0.10-1) ...
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Setting up libatomic1:arm64 (13.2.0-3) ...
Setting up libk5crypto3:arm64 (1.20.1-3) ...
Setting up libubsan1:arm64 (13.2.0-3) ...
Setting up libgcc-11-dev:arm64 (11.4.0-3) ...
Setting up libcrypt-dev:arm64 (1:4.4.36-2) ...
Setting up libkrb5-3:arm64 (1.20.1-3) ...
Setting up libgssapi-krb5-2:arm64 (1.20.1-3) ...
Setting up libtirpc3:arm64 (1.3.3+ds-1) ...
Setting up libtirpc-dev:arm64 (1.3.3+ds-1) ...
Setting up libnsl2:arm64 (1.3.0-2) ...
Setting up libnsl-dev:arm64 (1.3.0-2) ...
Setting up libc6-dev:arm64 (2.37-8) ...
Setting up libstdc++-11-dev:arm64 (11.4.0-3) ...
Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ...
Processing triggers for libc-bin (2.37-8) ...

+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (arm64 included in any all)

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

Kernel: Linux 6.1.0-9-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.27-1 (2023-05-08) amd64 (x86_64)
Toolchain package versions: binutils_2.41-5 dpkg-dev_1.22.0 g++-11_11.4.0-3 g++-13_13.2.0-3 gcc-11_11.4.0-3 gcc-13_13.2.0-3 libc6-dev_2.37-8 libstdc++-11-dev_11.4.0-3 libstdc++-13-dev_13.2.0-3 libstdc++-13-dev-arm64-cross_13.2.0-2cross1 libstdc++6_13.2.0-3 libstdc++6-arm64-cross_13.2.0-2cross1 linux-libc-dev_6.4.13-1
Package versions: adduser_3.137 apt_2.7.3 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-13 autotools-dev_20220109.1 base-files_13 base-passwd_3.6.1 bash_5.2.15-2+b4 binutils_2.41-5 binutils-aarch64-linux-gnu_2.41-5 binutils-common_2.41-5 binutils-x86-64-linux-gnu_2.41-5 bsdextrautils_2.39.2-1 bsdutils_1:2.39.2-1 build-essential_12.10 bzip2_1.0.8-5+b1 coreutils_9.1-1 cpp_4:13.2.0-1 cpp-11_11.4.0-3 cpp-13_13.2.0-3 cpp-13-aarch64-linux-gnu_13.2.0-2cross1 cpp-aarch64-linux-gnu_4:13.2.0-1 cross-config_2.6.20 crossbuild-essential-arm64_12.10 dash_0.5.12-6 debconf_1.5.82 debhelper_13.11.6 debian-archive-keyring_2023.4 debianutils_5.12 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.22.0 dpkg-cross_2.6.20 dpkg-dev_1.22.0 dwz_0.15-1 e2fsprogs_1.47.0-2+b1 fakeroot_1.32.1-1 file_1:5.45-2 findutils_4.9.0-5 g++_4:13.2.0-1 g++-11_11.4.0-3 g++-13_13.2.0-3 g++-13-aarch64-linux-gnu_13.2.0-2cross1 g++-aarch64-linux-gnu_4:13.2.0-1 gcc_4:13.2.0-1 gcc-11_11.4.0-3 gcc-11-base_11.4.0-3 gcc-12-base_12.3.0-8 gcc-13_13.2.0-3 gcc-13-aarch64-linux-gnu_13.2.0-2cross1 gcc-13-aarch64-linux-gnu-base_13.2.0-2cross1 gcc-13-base_13.2.0-3 gcc-13-cross-base_13.2.0-2cross1 gcc-9-base_9.5.0-4 gcc-aarch64-linux-gnu_4:13.2.0-1 gettext_0.21-13+b1 gettext-base_0.21-13+b1 gpgv_2.2.40-1.1 grep_3.11-3 groff-base_1.23.0-2 gzip_1.12-1 help2man_1.49.3 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.7.3 libarchive-zip-perl_1.68-1 libasan6_11.4.0-3 libasan8_13.2.0-3 libasan8-arm64-cross_13.2.0-2cross1 libatomic1_13.2.0-3 libatomic1-arm64-cross_13.2.0-2cross1 libattr1_1:2.5.1-4 libaudit-common_1:3.1.1-1 libaudit1_1:3.1.1-1 libbinutils_2.41-5 libblkid1_2.39.2-1 libbz2-1.0_1.0.8-5+b1 libc-bin_2.37-8 libc-dev-bin_2.37-8 libc6_2.37-8 libc6-arm64-cross_2.37-3cross1 libc6-dev_2.37-8 libc6-dev-arm64-cross_2.37-3cross1 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-4 libcc1-0_13.2.0-3 libcom-err2_1.47.0-2+b1 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+------------------------------------------------------------------------------+
| Build                                                                        |
+------------------------------------------------------------------------------+


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

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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
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zOrl+HbjgzU=
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-----END PGP SIGNATURE-----

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.arm64
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_US.UTF-8
LC_ALL=C.UTF-8
LOGNAME=crossqa
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=unstable-amd64-sbuild
SCHROOT_CHROOT_NAME=sid-amd64-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=1000
SCHROOT_GROUP=crossqa
SCHROOT_SESSION_ID=sid-amd64-sbuild-880fae83-75a9-4cdf-9548-c9c117816f14
SCHROOT_UID=1000
SCHROOT_USER=crossqa
SHELL=/bin/sh
USER=crossqa

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

Command: dpkg-buildpackage --sanitize-env -aarm64 -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 aarch64-linux-gnu does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture arm64
 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=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc BUILD_HOST=Debian "BUILD_TIME=14 October 2022" all doc
make[2]: Entering directory '/<<PKGBUILDDIR>>'
aarch64-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="\"`aarch64-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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
-I. -I third_party  \
-o hisat2-build-s hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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;
      |              ^~~~~~~~~~~~~~
aarch64-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="\"`aarch64-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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I. -I third_party  \
-o hisat2-build-l hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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;
      |              ^~~~~~~~~~~~~~
aarch64-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="\"`aarch64-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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2  -DBOWTIE2 -DNDEBUG -Wall \
-I. -I third_party   \
-o hisat2-align-s hisat2.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp  hisat2_main.cpp \
-lpthread   -Wl,-z,relro -Wl,-z,now
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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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;
      |                  ^~~~~~~~~~~~~~~
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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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 {
      |       ^~~~
aarch64-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="\"`aarch64-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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I. -I third_party   \
-o hisat2-align-l hisat2.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp  hisat2_main.cpp \
-lpthread   -Wl,-z,relro -Wl,-z,now
In file included from 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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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 ‘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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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 {
      |       ^~~~
aarch64-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="\"`aarch64-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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \
-I. -I third_party  -I . \
-o hisat2-inspect-s hisat2_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
In file included from hisat2_inspect.cpp:25:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:18: 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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
aarch64-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="\"`aarch64-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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \
-I. -I third_party  -I . \
-o hisat2-inspect-l hisat2_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
In file included from 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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-linux-gnu/include/c++/13/bits/unique_ptr.h:65:28: note: declared here
   65 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
aarch64-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="\"`aarch64-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 -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I. -I third_party  \
-o hisat2-repeat hisat2_repeat.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/13/memory:78,
                 from gfm.h:28:
/usr/aarch64-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/aarch64-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/aarch64-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/aarch64-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 2023-09-12T12:34:46Z

Finished
--------


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

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

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

Build Architecture: amd64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 71564
Build-Time: 410
Distribution: unstable
Fail-Stage: build
Foreign Architectures: arm64
Host Architecture: arm64
Install-Time: 15
Job: hisat2_2.2.1-4
Machine Architecture: amd64
Package: hisat2
Package-Time: 438
Source-Version: 2.2.1-4
Space: 71564
Status: attempted
Version: 2.2.1-4
--------------------------------------------------------------------------------
Finished at 2023-09-12T12:34:46Z
Build needed 00:07:18, 71564k disk space