sbuild (Debian sbuild) 0.78.1 (09 February 2019) on mjolnir

+==============================================================================+
| hisat2 2.2.1-3 (amd64)                       Fri, 08 Oct 2021 21:46:05 +0000 |
+==============================================================================+

Package: hisat2
Version: 2.2.1-3
Source Version: 2.2.1-3
Distribution: unstable
Machine Architecture: arm64
Host Architecture: amd64
Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any

I: NOTICE: Log filtering will replace 'var/run/schroot/mount/crossqa-sid-344db88e-bd19-43a3-89b3-b5ea00577d31' with '<<CHROOT>>'
I: NOTICE: Log filtering will replace 'build/hisat2-ykXqSq/resolver-s4o1Hl' with '<<RESOLVERDIR>>'

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

Get:1 http://mirror.einval.org/debian sid InRelease [165 kB]
Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index
Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index
Get:2 http://mirror.einval.org/debian sid/main Sources.diff/Index [63.6 kB]
Ign:2 http://mirror.einval.org/debian sid/main Sources.diff/Index
Ign:3 http://mirror.einval.org/debian sid/main arm64 Packages.diff/Index
Get:4 http://mirror.einval.org/debian sid/main amd64 Packages [8776 kB]
Get:5 http://mirror.einval.org/debian sid/main Sources [9252 kB]
Get:6 http://mirror.einval.org/debian sid/main arm64 Packages [8639 kB]
Fetched 26.8 MB in 7s (3813 kB/s)
Reading package lists...
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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://mirror.einval.org/debian sid/main hisat2 2.2.1-3 (dsc) [2129 B]
Get:2 http://mirror.einval.org/debian sid/main hisat2 2.2.1-3 (tar) [6761 kB]
Get:3 http://mirror.einval.org/debian sid/main hisat2 2.2.1-3 (diff) [29.0 kB]
Fetched 6792 kB in 0s (42.4 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/hisat2-ykXqSq/hisat2-2.2.1' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/hisat2-ykXqSq' with '<<BUILDDIR>>'

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


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

Merged Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64
Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:arm64, fakeroot:arm64, crossbuild-essential-amd64:arm64, libc-dev:amd64, libstdc++-dev:amd64
dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<<RESOLVERDIR>>/apt_archive/sbuild-build-depends-main-dummy.deb'.
Ign:1 copy:/<<RESOLVERDIR>>/apt_archive ./ InRelease
Get:2 copy:/<<RESOLVERDIR>>/apt_archive ./ Release [957 B]
Ign:3 copy:/<<RESOLVERDIR>>/apt_archive ./ Release.gpg
Get:4 copy:/<<RESOLVERDIR>>/apt_archive ./ Sources [439 B]
Get:5 copy:/<<RESOLVERDIR>>/apt_archive ./ Packages [518 B]
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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...
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu
  bsdextrautils cpp-10-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config
  crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-10-x86-64-linux-gnu g++-x86-64-linux-gnu
  gcc-10-base:amd64 gcc-10-cross-base gcc-10-x86-64-linux-gnu
  gcc-10-x86-64-linux-gnu-base gcc-11-base:amd64 gcc-11-cross-base
  gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man
  intltool-debian libarchive-zip-perl libasan6:amd64 libasan6-amd64-cross
  libatomic1:amd64 libatomic1-amd64-cross libc6:amd64 libc6-amd64-cross
  libc6-dev:amd64 libc6-dev-amd64-cross libcmark-gfm-extensions0 libcmark-gfm0
  libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl
  libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:amd64
  libgcc-10-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross
  libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libicu67
  libio-string-perl libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64
  libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64
  liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc
  libmagic1 libmpdec3 libncursesw6 libnsl-dev:amd64 libnsl2:amd64 libpipeline1
  libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
  libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 libsigsegv2
  libsimde-dev libsqlite3-0 libssl1.1:amd64 libstdc++-10-dev:amd64
  libstdc++-10-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross
  libsub-override-perl libtirpc-dev:amd64 libtirpc3:amd64 libtool
  libtsan0:amd64 libtsan0-amd64-cross libubsan1:amd64 libubsan1-amd64-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db media-types pandoc
  pandoc-data po-debconf python3 python3-minimal python3.9 python3.9-minimal
  readline-common sensible-utils ucf
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-10-locales
  cpp-doc dh-make binutils-multiarch g++-10-multilib-x86-64-linux-gnu
  gcc-10-doc gcc-10-multilib-x86-64-linux-gnu manpages-dev flex bison
  gdb-x86-64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev
  groff glibc-doc:amd64 libc-l10n:amd64 locales:amd64 libnss-nis:amd64
  libnss-nisplus:amd64 manpages-dev:amd64 krb5-doc:amd64 krb5-user:amd64
  libstdc++-10-doc:amd64 libtool-doc gfortran | fortran95-compiler gcj-jdk
  libyaml-shell-perl m4-doc apparmor less www-browser
  texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc
  texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python
  ruby r-base-core libjs-mathjax node-katex citation-style-language-styles
  libmail-box-perl python3-doc python3-tk python3-venv python3.9-venv
  python3.9-doc binfmt-support readline-doc
Recommended packages:
  curl | wget | lynx libidn2-0:amd64 libarchive-cpio-perl krb5-locales:amd64
  libgpm2 ca-certificates libltdl-dev libwww-perl libxml-sax-expat-perl
  libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev binutils-x86-64-linux-gnu
  bsdextrautils cpp-10-x86-64-linux-gnu cpp-x86-64-linux-gnu cross-config
  crossbuild-essential-amd64 debhelper dh-autoreconf dh-strip-nondeterminism
  dpkg-cross dwz file g++-10-x86-64-linux-gnu g++-x86-64-linux-gnu
  gcc-10-base:amd64 gcc-10-cross-base gcc-10-x86-64-linux-gnu
  gcc-10-x86-64-linux-gnu-base gcc-11-base:amd64 gcc-11-cross-base
  gcc-x86-64-linux-gnu gettext gettext-base groff-base help2man
  intltool-debian libarchive-zip-perl libasan6:amd64 libasan6-amd64-cross
  libatomic1:amd64 libatomic1-amd64-cross libc6:amd64 libc6-amd64-cross
  libc6-dev:amd64 libc6-dev-amd64-cross libcmark-gfm-extensions0 libcmark-gfm0
  libcom-err2:amd64 libconfig-auto-perl libconfig-inifiles-perl
  libcrypt-dev:amd64 libcrypt1:amd64 libdebhelper-perl
  libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-10-dev:amd64
  libgcc-10-dev-amd64-cross libgcc-s1:amd64 libgcc-s1-amd64-cross
  libgomp1:amd64 libgomp1-amd64-cross libgssapi-krb5-2:amd64 libicu67
  libio-string-perl libitm1:amd64 libitm1-amd64-cross libk5crypto3:amd64
  libkeyutils1:amd64 libkrb5-3:amd64 libkrb5support0:amd64
  liblocale-gettext-perl liblsan0:amd64 liblsan0-amd64-cross libmagic-mgc
  libmagic1 libmpdec3 libncursesw6 libnsl-dev:amd64 libnsl2:amd64 libpipeline1
  libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib
  libquadmath0:amd64 libquadmath0-amd64-cross libreadline8 libsigsegv2
  libsimde-dev libsqlite3-0 libssl1.1:amd64 libstdc++-10-dev:amd64
  libstdc++-10-dev-amd64-cross libstdc++6:amd64 libstdc++6-amd64-cross
  libsub-override-perl libtirpc-dev:amd64 libtirpc3:amd64 libtool
  libtsan0:amd64 libtsan0-amd64-cross libubsan1:amd64 libubsan1-amd64-cross
  libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl
  libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl
  linux-libc-dev:amd64 linux-libc-dev-amd64-cross m4 man-db media-types pandoc
  pandoc-data po-debconf python3 python3-minimal python3.9 python3.9-minimal
  readline-common sbuild-build-depends-main-dummy:amd64 sensible-utils ucf
0 upgraded, 124 newly installed, 0 to remove and 0 not upgraded.
Need to get 236 MB of archives.
After this operation, 1143 MB of additional disk space will be used.
Get:1 copy:/<<RESOLVERDIR>>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [948 B]
Get:2 http://mirror.einval.org/debian sid/main arm64 bsdextrautils arm64 2.37.2-3 [143 kB]
Get:3 http://mirror.einval.org/debian sid/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB]
Get:4 http://mirror.einval.org/debian sid/main arm64 groff-base arm64 1.22.4-7 [883 kB]
Get:5 http://mirror.einval.org/debian sid/main arm64 libpipeline1 arm64 1.5.3-1 [33.0 kB]
Get:6 http://mirror.einval.org/debian sid/main arm64 man-db arm64 2.9.4-2 [1336 kB]
Get:7 http://mirror.einval.org/debian sid/main arm64 liblocale-gettext-perl arm64 1.07-4+b1 [18.9 kB]
Get:8 http://mirror.einval.org/debian sid/main arm64 libpython3.9-minimal arm64 3.9.7-4 [800 kB]
Get:9 http://mirror.einval.org/debian sid/main arm64 libexpat1 arm64 2.4.1-2+b1 [90.3 kB]
Get:10 http://mirror.einval.org/debian sid/main arm64 python3.9-minimal arm64 3.9.7-4 [1885 kB]
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Get:12 http://mirror.einval.org/debian sid/main arm64 media-types all 4.0.0 [30.3 kB]
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Get:14 http://mirror.einval.org/debian sid/main arm64 libncursesw6 arm64 6.2+20210905-1 [122 kB]
Get:15 http://mirror.einval.org/debian sid/main arm64 readline-common all 8.1-2 [73.8 kB]
Get:16 http://mirror.einval.org/debian sid/main arm64 libreadline8 arm64 8.1-2 [160 kB]
Get:17 http://mirror.einval.org/debian sid/main arm64 libsqlite3-0 arm64 3.36.0-2 [768 kB]
Get:18 http://mirror.einval.org/debian sid/main arm64 libpython3.9-stdlib arm64 3.9.7-4 [1663 kB]
Get:19 http://mirror.einval.org/debian sid/main arm64 python3.9 arm64 3.9.7-4 [480 kB]
Get:20 http://mirror.einval.org/debian sid/main arm64 libpython3-stdlib arm64 3.9.2-3 [21.4 kB]
Get:21 http://mirror.einval.org/debian sid/main arm64 python3 arm64 3.9.2-3 [37.9 kB]
Get:22 http://mirror.einval.org/debian sid/main amd64 gcc-10-base amd64 10.3.0-11 [206 kB]
Get:23 http://mirror.einval.org/debian sid/main amd64 gcc-11-base amd64 11.2.0-8 [205 kB]
Get:24 http://mirror.einval.org/debian sid/main arm64 sensible-utils all 0.0.17 [21.5 kB]
Get:25 http://mirror.einval.org/debian sid/main arm64 libmagic-mgc arm64 1:5.39-3 [273 kB]
Get:26 http://mirror.einval.org/debian sid/main arm64 libmagic1 arm64 1:5.39-3 [121 kB]
Get:27 http://mirror.einval.org/debian sid/main arm64 file arm64 1:5.39-3 [69.1 kB]
Get:28 http://mirror.einval.org/debian sid/main arm64 gettext-base arm64 0.21-4 [173 kB]
Get:29 http://mirror.einval.org/debian sid/main arm64 ucf all 3.0043 [74.0 kB]
Get:30 http://mirror.einval.org/debian sid/main arm64 libsigsegv2 arm64 2.13-1 [34.7 kB]
Get:31 http://mirror.einval.org/debian sid/main arm64 m4 arm64 1.4.18-5 [199 kB]
Get:32 http://mirror.einval.org/debian sid/main arm64 autoconf all 2.71-2 [343 kB]
Get:33 http://mirror.einval.org/debian sid/main arm64 autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:34 http://mirror.einval.org/debian sid/main arm64 automake all 1:1.16.4-2 [819 kB]
Get:35 http://mirror.einval.org/debian sid/main arm64 autopoint all 0.21-4 [510 kB]
Get:36 http://mirror.einval.org/debian sid/main arm64 gcc-10-x86-64-linux-gnu-base arm64 10.3.0-8cross1 [205 kB]
Get:37 http://mirror.einval.org/debian sid/main arm64 cpp-10-x86-64-linux-gnu arm64 10.3.0-8cross1 [46.3 MB]
Get:38 http://mirror.einval.org/debian sid/main arm64 cpp-x86-64-linux-gnu arm64 4:10.2.1-1 [16.8 kB]
Get:39 http://mirror.einval.org/debian sid/main arm64 cross-config all 2.6.18+nmu2 [31.7 kB]
Get:40 http://mirror.einval.org/debian sid/main arm64 binutils-x86-64-linux-gnu arm64 2.37-7 [2046 kB]
Get:41 http://mirror.einval.org/debian sid/main arm64 gcc-10-cross-base all 10.3.0-8cross1 [200 kB]
Get:42 http://mirror.einval.org/debian sid/main arm64 gcc-11-cross-base all 11.2.0-5cross1 [201 kB]
Get:43 http://mirror.einval.org/debian sid/main arm64 libgcc-s1-amd64-cross all 11.2.0-5cross1 [42.0 kB]
Get:44 http://mirror.einval.org/debian sid/main arm64 libgomp1-amd64-cross all 11.2.0-5cross1 [104 kB]
Get:45 http://mirror.einval.org/debian sid/main arm64 libitm1-amd64-cross all 11.2.0-5cross1 [25.5 kB]
Get:46 http://mirror.einval.org/debian sid/main arm64 libatomic1-amd64-cross all 11.2.0-5cross1 [8776 B]
Get:47 http://mirror.einval.org/debian sid/main arm64 libasan6-amd64-cross all 11.2.0-5cross1 [2041 kB]
Get:48 http://mirror.einval.org/debian sid/main arm64 liblsan0-amd64-cross all 11.2.0-5cross1 [884 kB]
Get:49 http://mirror.einval.org/debian sid/main arm64 libtsan0-amd64-cross all 11.2.0-5cross1 [2007 kB]
Get:50 http://mirror.einval.org/debian sid/main arm64 libc6-amd64-cross all 2.32-1cross4 [1570 kB]
Get:51 http://mirror.einval.org/debian sid/main arm64 libstdc++6-amd64-cross all 11.2.0-5cross1 [535 kB]
Get:52 http://mirror.einval.org/debian sid/main arm64 libubsan1-amd64-cross all 11.2.0-5cross1 [832 kB]
Get:53 http://mirror.einval.org/debian sid/main arm64 libquadmath0-amd64-cross all 11.2.0-5cross1 [144 kB]
Get:54 http://mirror.einval.org/debian sid/main arm64 libgcc-10-dev-amd64-cross all 10.3.0-8cross1 [2323 kB]
Get:55 http://mirror.einval.org/debian sid/main arm64 gcc-10-x86-64-linux-gnu arm64 10.3.0-8cross1 [52.3 MB]
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Get:57 http://mirror.einval.org/debian sid/main arm64 linux-libc-dev-amd64-cross all 5.10.46-4cross4 [1468 kB]
Get:58 http://mirror.einval.org/debian sid/main arm64 libc6-dev-amd64-cross all 2.32-1cross4 [2248 kB]
Get:59 http://mirror.einval.org/debian sid/main arm64 libstdc++-10-dev-amd64-cross all 10.3.0-8cross1 [1733 kB]
Get:60 http://mirror.einval.org/debian sid/main arm64 g++-10-x86-64-linux-gnu arm64 10.3.0-8cross1 [49.3 MB]
Get:61 http://mirror.einval.org/debian sid/main arm64 g++-x86-64-linux-gnu arm64 4:10.2.1-1 [1180 B]
Get:62 http://mirror.einval.org/debian sid/main arm64 libconfig-inifiles-perl all 3.000003-1 [52.1 kB]
Get:63 http://mirror.einval.org/debian sid/main arm64 libio-string-perl all 1.08-3.1 [11.8 kB]
Get:64 http://mirror.einval.org/debian sid/main arm64 libicu67 arm64 67.1-7 [8467 kB]
Get:65 http://mirror.einval.org/debian sid/main arm64 libxml2 arm64 2.9.12+dfsg-5 [632 kB]
Get:66 http://mirror.einval.org/debian sid/main arm64 libxml-namespacesupport-perl all 1.12-1.1 [14.9 kB]
Get:67 http://mirror.einval.org/debian sid/main arm64 libxml-sax-base-perl all 1.09-1.1 [20.7 kB]
Get:68 http://mirror.einval.org/debian sid/main arm64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB]
Get:69 http://mirror.einval.org/debian sid/main arm64 libxml-libxml-perl arm64 2.0134+dfsg-2+b1 [326 kB]
Get:70 http://mirror.einval.org/debian sid/main arm64 libxml-simple-perl all 2.25-1 [72.0 kB]
Get:71 http://mirror.einval.org/debian sid/main arm64 libyaml-perl all 1.30-1 [67.7 kB]
Get:72 http://mirror.einval.org/debian sid/main arm64 libconfig-auto-perl all 0.44-1.1 [19.0 kB]
Get:73 http://mirror.einval.org/debian sid/main arm64 libfile-which-perl all 1.23-1 [16.6 kB]
Get:74 http://mirror.einval.org/debian sid/main arm64 libfile-homedir-perl all 1.006-1 [43.8 kB]
Get:75 http://mirror.einval.org/debian sid/main arm64 libdebian-dpkgcross-perl all 2.6.18+nmu2 [30.6 kB]
Get:76 http://mirror.einval.org/debian sid/main arm64 dpkg-cross all 2.6.18+nmu2 [40.9 kB]
Get:77 http://mirror.einval.org/debian sid/main arm64 crossbuild-essential-amd64 all 12.9 [6708 B]
Get:78 http://mirror.einval.org/debian sid/main arm64 libdebhelper-perl all 13.5.2 [192 kB]
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Get:90 http://mirror.einval.org/debian sid/main arm64 debhelper all 13.5.2 [1056 kB]
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Get:102 http://mirror.einval.org/debian sid/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB]
Get:103 http://mirror.einval.org/debian sid/main amd64 libssl1.1 amd64 1.1.1l-1 [1555 kB]
Get:104 http://mirror.einval.org/debian sid/main amd64 libkrb5-3 amd64 1.18.3-7 [363 kB]
Get:105 http://mirror.einval.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.18.3-7 [165 kB]
Get:106 http://mirror.einval.org/debian sid/main amd64 libtirpc3 amd64 1.3.2-2 [83.9 kB]
Get:107 http://mirror.einval.org/debian sid/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB]
Get:108 http://mirror.einval.org/debian sid/main amd64 libtirpc-dev amd64 1.3.2-2 [190 kB]
Get:109 http://mirror.einval.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB]
Get:110 http://mirror.einval.org/debian sid/main amd64 libc6-dev amd64 2.32-4 [2251 kB]
Get:111 http://mirror.einval.org/debian sid/main arm64 libcmark-gfm0 arm64 0.29.0.gfm.0-6 [108 kB]
Get:112 http://mirror.einval.org/debian sid/main arm64 libcmark-gfm-extensions0 arm64 0.29.0.gfm.0-6 [45.4 kB]
Get:113 http://mirror.einval.org/debian sid/main amd64 libgomp1 amd64 11.2.0-8 [106 kB]
Get:114 http://mirror.einval.org/debian sid/main amd64 libitm1 amd64 11.2.0-8 [26.0 kB]
Get:115 http://mirror.einval.org/debian sid/main amd64 liblsan0 amd64 11.2.0-8 [885 kB]
Get:116 http://mirror.einval.org/debian sid/main amd64 libtsan0 amd64 11.2.0-8 [2014 kB]
Get:117 http://mirror.einval.org/debian sid/main amd64 libstdc++6 amd64 11.2.0-8 [577 kB]
Get:118 http://mirror.einval.org/debian sid/main amd64 libubsan1 amd64 11.2.0-8 [833 kB]
Get:119 http://mirror.einval.org/debian sid/main amd64 libquadmath0 amd64 11.2.0-8 [145 kB]
Get:120 http://mirror.einval.org/debian sid/main amd64 libgcc-10-dev amd64 10.3.0-11 [2323 kB]
Get:121 http://mirror.einval.org/debian sid/main arm64 libsimde-dev all 0.7.2-4 [259 kB]
Get:122 http://mirror.einval.org/debian sid/main amd64 libstdc++-10-dev amd64 10.3.0-11 [1750 kB]
Get:123 http://mirror.einval.org/debian sid/main arm64 pandoc-data all 2.9.2.1-1 [376 kB]
Get:124 http://mirror.einval.org/debian sid/main arm64 pandoc arm64 2.9.2.1-1+b2 [22.7 MB]
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+------------------------------------------------------------------------------+
| Check architectures                                                          |
+------------------------------------------------------------------------------+

Arch check ok (amd64 included in any all)

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

Kernel: Linux 5.9.0-0.bpo.2-arm64 #1 SMP Debian 5.9.6-1~bpo10+1 (2020-11-19) arm64 (aarch64)
Toolchain package versions: binutils_2.37-7 dpkg-dev_1.20.9 g++-10_10.3.0-11 gcc-10_10.3.0-11 libc6-dev_2.32-4 libstdc++-10-dev_10.3.0-11 libstdc++-10-dev-amd64-cross_10.3.0-8cross1 libstdc++6_11.2.0-8 libstdc++6-amd64-cross_11.2.0-5cross1 linux-libc-dev_5.14.9-2
Package versions: adduser_3.118 apt_2.3.9 autoconf_2.71-2 automake_1:1.16.4-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_12 base-passwd_3.5.52 bash_5.1-3+b2 binutils_2.37-7 binutils-aarch64-linux-gnu_2.37-7 binutils-common_2.37-7 binutils-x86-64-linux-gnu_2.37-7 bsdextrautils_2.37.2-3 bsdutils_1:2.37.2-3 build-essential_12.9 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.1-1 cpp-10_10.3.0-11 cpp-10-x86-64-linux-gnu_10.3.0-8cross1 cpp-x86-64-linux-gnu_4:10.2.1-1 cross-config_2.6.18+nmu2 crossbuild-essential-amd64_12.9 dash_0.5.11+git20210120+802ebd4-1 debconf_1.5.77 debhelper_13.5.2 debian-archive-keyring_2021.1.1 debianutils_5.5-1 dh-autoreconf_20 dh-strip-nondeterminism_1.12.0-1 diffutils_1:3.7-5 dpkg_1.20.9 dpkg-cross_2.6.18+nmu2 dpkg-dev_1.20.9 dwz_0.14-1 fakeroot_1.26-1 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1 g++-10_10.3.0-11 g++-10-x86-64-linux-gnu_10.3.0-8cross1 g++-x86-64-linux-gnu_4:10.2.1-1 gcc_4:10.2.1-1 gcc-10_10.3.0-11 gcc-10-base_10.3.0-11 gcc-10-cross-base_10.3.0-8cross1 gcc-10-x86-64-linux-gnu_10.3.0-8cross1 gcc-10-x86-64-linux-gnu-base_10.3.0-8cross1 gcc-11-base_11.2.0-8 gcc-11-cross-base_11.2.0-5cross1 gcc-x86-64-linux-gnu_4:10.2.1-1 gettext_0.21-4 gettext-base_0.21-4 gpgv_2.2.27-2 grep_3.7-1 groff-base_1.22.4-7 gzip_1.10-4 help2man_1.48.5 hostname_3.23 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.9 libarchive-zip-perl_1.68-1 libasan6_11.2.0-8 libasan6-amd64-cross_11.2.0-5cross1 libatomic1_11.2.0-8 libatomic1-amd64-cross_11.2.0-5cross1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.5-1 libaudit1_1:3.0.5-1 libbinutils_2.37-7 libblkid1_2.37.2-3 libbz2-1.0_1.0.8-4 libc-bin_2.32-4 libc-dev-bin_2.32-4 libc6_2.32-4 libc6-amd64-cross_2.32-1cross4 libc6-dev_2.32-4 libc6-dev-amd64-cross_2.32-1cross4 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-8 libcmark-gfm-extensions0_0.29.0.gfm.0-6 libcmark-gfm0_0.29.0.gfm.0-6 libcom-err2_1.46.4-1 libconfig-auto-perl_0.44-1.1 libconfig-inifiles-perl_3.000003-1 libcrypt-dev_1:4.4.25-2 libcrypt1_1:4.4.25-2 libctf-nobfd0_2.37-7 libctf0_2.37-7 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.260 libdebhelper-perl_13.5.2 libdebian-dpkgcross-perl_2.6.18+nmu2 libdpkg-perl_1.20.9 libelf1_0.185-2 libexpat1_2.4.1-2+b1 libfakeroot_1.26-1 libffi8_3.4.2-2 libfile-homedir-perl_1.006-1 libfile-stripnondeterminism-perl_1.12.0-1 libfile-which-perl_1.23-1 libgcc-10-dev_10.3.0-11 libgcc-10-dev-amd64-cross_10.3.0-8cross1 libgcc-s1_11.2.0-8 libgcc-s1-amd64-cross_11.2.0-5cross1 libgcrypt20_1.9.4-3+b1 libgdbm-compat4_1.21-1 libgdbm6_1.21-1 libgmp10_2:6.2.1+dfsg-2 libgnutls30_3.7.2-2 libgomp1_11.2.0-8 libgomp1-amd64-cross_11.2.0-5cross1 libgpg-error0_1.42-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libio-string-perl_1.08-3.1 libisl23_0.23-1 libitm1_11.2.0-8 libitm1-amd64-cross_11.2.0-5cross1 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 liblocale-gettext-perl_1.07-4+b1 liblsan0_11.2.0-8 liblsan0-amd64-cross_11.2.0-5cross1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmount1_2.37.2-3 libmpc3_1.2.0-1 libmpdec3_2.5.1-2 libmpfr6_4.1.0-3 libncursesw6_6.2+20210905-1 libnettle8_3.7.3-1 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.0-3 libpam-modules_1.4.0-10 libpam-modules-bin_1.4.0-10 libpam-runtime_1.4.0-10 libpam0g_1.4.0-10 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libpipeline1_1.5.3-1 libpython3-stdlib_3.9.2-3 libpython3.9-minimal_3.9.7-4 libpython3.9-stdlib_3.9.7-4 libquadmath0_11.2.0-8 libquadmath0-amd64-cross_11.2.0-5cross1 libreadline8_8.1-2 libseccomp2_2.5.2-2 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b2 libsepol1_3.1-1 libsigsegv2_2.13-1 libsimde-dev_0.7.2-4 libsmartcols1_2.37.2-3 libsqlite3-0_3.36.0-2 libssl1.1_1.1.1l-1 libstdc++-10-dev_10.3.0-11 libstdc++-10-dev-amd64-cross_10.3.0-8cross1 libstdc++6_11.2.0-8 libstdc++6-amd64-cross_11.2.0-5cross1 libsub-override-perl_0.09-2 libsystemd0_247.9-4 libtasn1-6_4.17.0-2 libtinfo6_6.2+20210905-1 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libtsan0_11.2.0-8 libtsan0-amd64-cross_11.2.0-5cross1 libubsan1_11.2.0-8 libubsan1-amd64-cross_11.2.0-5cross1 libuchardet0_0.0.7-1 libudev1_247.9-4 libunistring2_0.9.10-6 libuuid1_2.37.2-3 libxml-libxml-perl_2.0134+dfsg-2+b1 libxml-namespacesupport-perl_1.12-1.1 libxml-sax-base-perl_1.09-1.1 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-1 libxml2_2.9.12+dfsg-5 libxxhash0_0.8.0-2 libyaml-perl_1.30-1 libzstd1_1.4.8+dfsg-3 linux-libc-dev_5.14.9-2 linux-libc-dev-amd64-cross_5.10.46-4cross4 login_1:4.8.1-1 lsb-base_11.1.0 m4_1.4.18-5 make_4.3-4.1 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.37.2-3 ncurses-base_6.2+20210905-1 ncurses-bin_6.2+20210905-1 pandoc_2.9.2.1-1+b2 pandoc-data_2.9.2.1-1 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-6 perl-base_5.32.1-6 perl-modules-5.32_5.32.1-6 po-debconf_1.0.21+nmu1 python3_3.9.2-3 python3-minimal_3.9.2-3 python3.9_3.9.7-4 python3.9-minimal_3.9.7-4 readline-common_8.1-2 rpcsvc-proto_1.4.2-4 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sysvinit-utils_3.00-1 tar_1.34+dfsg-1 tzdata_2021c-2 ucf_3.0043 util-linux_2.37.2-3 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2

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


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

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

Format: 3.0 (quilt)
Source: hisat2
Binary: hisat2, python3-hisat2
Architecture: any all
Version: 2.2.1-3
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: 4.6.0
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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 a43c51606d45c0cc9f27bd5c9a0b862d62701840 29000 hisat2_2.2.1-3.debian.tar.xz
Checksums-Sha256:
 f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599 6761242 hisat2_2.2.1.orig.tar.gz
 5efee24872fdea71d3b22568bb400971c8c00180148375c87547119763a48528 29000 hisat2_2.2.1-3.debian.tar.xz
Files:
 0d1fcfcaf7ba1e64eb68006bba5a3855 6761242 hisat2_2.2.1.orig.tar.gz
 ffded91d9506d63eaa2a3bd1c5289fac 29000 hisat2_2.2.1-3.debian.tar.xz

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gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.TMYVAbho/trustedkeys.kbx': General error
gpgv: Signature made Tue Sep 28 08:40:16 2021 UTC
gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv:                issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./hisat2_2.2.1-3.dsc
dpkg-source: info: extracting hisat2 in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz
dpkg-source: info: unpacking hisat2_2.2.1-3.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

+------------------------------------------------------------------------------+
| Starting Timed Build Commands                                                |
+------------------------------------------------------------------------------+


ulimit -c
---------

0

I: Finished running 'ulimit -c'.

Finished processing commands.
--------------------------------------------------------------------------------

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

APT_CONFIG=/var/lib/sbuild/apt.conf
CONFIG_SITE=/etc/dpkg-cross/cross-config.amd64
DEB_BUILD_OPTIONS=nocheck
HOME=/sbuild-nonexistent
LANG=en_GB.UTF-8
LC_ALL=C.UTF-8
LOGNAME=helmutg
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=crossqa-sid
SCHROOT_CHROOT_NAME=crossqa-sid
SCHROOT_COMMAND=env
SCHROOT_GID=1002
SCHROOT_GROUP=helmutg
SCHROOT_SESSION_ID=crossqa-sid-344db88e-bd19-43a3-89b3-b5ea00577d31
SCHROOT_UID=1002
SCHROOT_USER=helmutg
SHELL=/bin/sh
USER=helmutg

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

Command: dpkg-buildpackage -aamd64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1
dpkg-buildpackage: info: source package hisat2
dpkg-buildpackage: info: source version 2.2.1-3
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-architecture: warning: specified GNU system type x86_64-linux-gnu does not match CC system type aarch64-linux-gnu, try setting a correct CC environment variable
 dpkg-source --before-build .
dpkg-buildpackage: info: host architecture amd64
 debian/rules clean
dh clean
   dh_auto_clean
	make -j1 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-repeat hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug hisat2-repeat-debug \
hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-repeat.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe hisat2-repeat-debug.exe \
hisat2-src.zip hisat2-bin.zip
rm -f core.* .tmp.head
rm -rf *.dSYM
rm -rf .ht2lib-obj*
rm -f libhisat2lib*.a libhisat2lib*.so
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_clean
 debian/rules binary-arch
dh binary-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
   debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build --  BUILD_HOST='Debian' BUILD_TIME="28 September 2021" all doc
	make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=x86_64-linux-gnu-pkg-config CXX=x86_64-linux-gnu-g\+\+ CC=x86_64-linux-gnu-gcc BUILD_HOST=Debian "BUILD_TIME=28 September 2021" all doc
make[2]: Entering directory '/<<PKGBUILDDIR>>'
x86_64-linux-gnu-g++ -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"28 September 2021\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \
-I. -I third_party  \
-o hisat2-build-s hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
In file included from hisat2_build.cpp:35:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from hisat2_build.cpp:30:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hisat2_build.cpp:35:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from hisat2_build.cpp:30:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hisat2_build.cpp:35:
gfm.h: In instantiation of ‘void GFM<index_t>::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, const string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, bool) [with TStr = SString<char>; index_t = unsigned int; std::string = std::__cxx11::basic_string<char>; std::ofstream = std::basic_ofstream<char>; uint32_t = unsigned int]’:
gfm.h:1039:23:   required from ‘GFM<index_t>::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
hgfm.h:1989:14:   required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; TIndexOffU = unsigned int; uint32_t = unsigned int]’
hisat2_build.cpp:535:15:   required from ‘void driver(const string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56:   required from here
gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable]
 2167 |                         index_t template_len = 0;
      |                                 ^~~~~~~~~~~~
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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |   uint64_t origBufOff = bufOff;
      |            ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |  bool binarySearched = false;
      |       ^~~~~~~~~~~~~~
x86_64-linux-gnu-g++ -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"28 September 2021\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I. -I third_party  \
-o hisat2-build-l hisat2_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
In file included from hisat2_build.cpp:35:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from hisat2_build.cpp:30:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hisat2_build.cpp:35:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from hisat2_build.cpp:30:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hisat2_build.cpp:35:
gfm.h: In instantiation of ‘void GFM<index_t>::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, const string&, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, bool) [with TStr = SString<char>; index_t = long 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 string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string<char>; uint32_t = unsigned int]’
hgfm.h:1989:14:   required from ‘HGFM<index_t, local_index_t>::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList<FileBuf*>&, EList<RefRecord>&, index_t, const RefReadInParams&, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString<char>; index_t = long 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 string&, EList<std::__cxx11::basic_string<char> >&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int, bool, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*, EList<RefRecord>*, EList<std::__cxx11::basic_string<char> >*) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2_build.cpp:801:56:   required from here
gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable]
 2167 |                         index_t template_len = 0;
      |                                 ^~~~~~~~~~~~
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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |   uint64_t origBufOff = bufOff;
      |            ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |  bool binarySearched = false;
      |       ^~~~~~~~~~~~~~
x86_64-linux-gnu-g++ -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"28 September 2021\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2  -DBOWTIE2 -DNDEBUG -Wall \
-I. -I third_party   \
-o hisat2-align-s hisat2.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp  hisat2_main.cpp \
-lpthread   -Wl,-z,relro -Wl,-z,now
In file included from hgfm.h:24,
                 from hisat2.cpp:33:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hgfm.h:24,
                 from hisat2.cpp:33:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1823:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1823 |  auto_ptr<Presets> presets(new PresetsV0());
      |  ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3167:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 3167 |  auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
      |  ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3168:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 3168 |  auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
      |  ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3189:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 3189 |  auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
      |  ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’:
hisat2.cpp:4035:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 4035 |         auto_ptr<BitPairReference> refs(
      |         ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:3556:58:   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())
      |                                                                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from hgfm.h:24,
                 from hisat2.cpp:33:
gfm.h: In instantiation of ‘void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = unsigned int]’:
hisat2.cpp:3815:17:   required from ‘void driver(const char*, const string&, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2.cpp:4351:51:   required from here
gfm.h: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,
                 from spliced_aligner.h:23,
                 from hisat2.cpp:46:
group_walk.h: In instantiation of ‘std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’:
group_walk.h:1517:14:   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:3556:58:   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++) {
      |                                                    ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’:
hi_aligner.h:717:28:   required from ‘static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:2337:47:   required from ‘static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’
hi_aligner.h:5692:54:   required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4107:39:   required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3556:58:   required from here
hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘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) {
      |                        ~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from aligner_seed2.h:109,
                 from aligner_driver.h:78,
                 from hi_aligner.h:41,
                 from spliced_aligner.h:23,
                 from hisat2.cpp:46:
group_walk.h: In instantiation of ‘std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’:
group_walk.h:494:14:   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:3556:58:   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()) {
      |                    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, Haplotype<index_t>&, EList<std::pair<_FIter, _FIter> >&, index_t, bool, bool) [with index_t = unsigned int]’:
hi_aligner.h:2915:39:   required from ‘static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:717:28:   required from ‘static index_t GenomeHit<index_t>::alignWithALTs(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars<index_t>&, index_t, int, index_t, bool, const GraphPolicy&, EList<Edit>&, ELList<std::pair<_FIter, _FIter> >&, EList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’
hi_aligner.h:2337:47:   required from ‘static bool GenomeHit<index_t>::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars<index_t>&, EList<GenomeHit<index_t> >&, const Read&, const GFM<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’
hi_aligner.h:5692:54:   required from ‘bool HI_Aligner<index_t, local_index_t>::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’
hi_aligner.h:4107:39:   required from ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]’
hisat2.cpp:3556:58:   required from here
hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘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) {
      |                        ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from hisat2.cpp:46:
spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’:
spliced_aligner.h:331:9:   required from here
spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable]
  408 |             bool another_spliced = false;
      |                  ^~~~~~~~~~~~~~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘bool GenomeHit<index_t>::combineWith(const GenomeHit<index_t>&, const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = unsigned int; TAlScore = long int]’:
spliced_aligner.h:494:60:   required from ‘int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’
spliced_aligner.h:331:9:   required from here
hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long unsigned int’} and ‘char’ [-Wsign-compare]
 1926 |                     if(alt.seq == rdc) {
      |                        ~~~~~~~~^~~~~~
In file included from gfm.h:59,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
repeat.h: In member function ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = unsigned int; local_index_t = short unsigned int]’:
repeat.h:41:20: warning: ‘cmp.RepeatCoord<unsigned int>::fw’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   41 |         if(fw != o.fw)
      |                  ~~^~
repeat.h:43:26: warning: ‘cmp.RepeatCoord<unsigned int>::alleleID’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   43 |         if(alleleID != o.alleleID)
      |                        ~~^~~~~~~~
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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |   uint64_t origBufOff = bufOff;
      |            ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |  bool binarySearched = false;
      |       ^~~~~~~~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_seed2.cpp:22:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_seed2.cpp:22:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from aligner_result.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from aligner_result.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from aln_sink.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from aln_sink.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from unique.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from unique.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from splice_site.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from splice_site.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from splice_site.cpp:20:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from splice_site.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM<unsigned int>&, const EList<ALT<unsigned int> >&)’:
splice_site.cpp:717:59: warning: ‘?:’ using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context]
  717 |             exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC);
      |                                                 ~~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from edit.h:29,
                 from splice_site.cpp:20:
ds.h: In instantiation of ‘void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’:
splice_site.cpp:722:59:   required from here
ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  663 |   std::memcpy(list_ + cur_, l, bytes);
      |   ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from edit.h:30,
                 from splice_site.cpp:20:
splice_site.h:377:7: note: ‘class Exon’ declared here
  377 | class Exon {
      |       ^~~~
x86_64-linux-gnu-g++ -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"28 September 2021\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2  -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I. -I third_party   \
-o hisat2-align-l hisat2.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp  hisat2_main.cpp \
-lpthread   -Wl,-z,relro -Wl,-z,now
In file included from hgfm.h:24,
                 from hisat2.cpp:33:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hgfm.h:24,
                 from hisat2.cpp:33:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void parseOptions(int, const char**)’:
hisat2.cpp:1823:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1823 |  auto_ptr<Presets> presets(new PresetsV0());
      |  ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’:
hisat2.cpp:3167:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 3167 |  auto_ptr<PatternSourcePerThreadFactory> patsrcFact(createPatsrcFactory(patsrc, tid));
      |  ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3168:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 3168 |  auto_ptr<PatternSourcePerThread> ps(patsrcFact->create());
      |  ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp:3189:2: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 3189 |  auto_ptr<Mapq> bmapq(new_mapq(mapqv, scoreMin, sc));
      |  ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’:
hisat2.cpp:4035:9: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 4035 |         auto_ptr<BitPairReference> refs(
      |         ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:3556:58:   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:3556:58:   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:3556:58:   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())
      |                                                                           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
In file included from hgfm.h:24,
                 from hisat2.cpp:33:
gfm.h: In instantiation of ‘void GFM<index_t>::checkOrigs(const EList<SString<char> >&, bool) const [with index_t = long unsigned int]’:
hisat2.cpp:3815:17:   required from ‘void driver(const char*, const string&, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’
hisat2.cpp:4351:51:   required from here
gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable]
 6935 |         int lastorig = -1;
      |             ^~~~~~~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘index_t HI_Aligner<index_t, local_index_t>::getAnchorHits(const GFM<index_t>&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, RandomSource&, index_t, bool, EList<GenomeHit<index_t> >&, index_t, SharedTempVars<index_t>&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long 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:3556:58:   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:3556:58:   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,
                 from spliced_aligner.h:23,
                 from hisat2.cpp:46:
group_walk.h: In instantiation of ‘std::pair<int, int> GWState<index_t, T>::advance(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, EList<GWState<index_t, T>, S>&, GroupWalkState<index_t>&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’:
group_walk.h:1517:14:   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:3556:58:   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++) {
      |                                                    ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘static index_t GenomeHit<index_t>::alignWithALTs_recur(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList<SStringExpandable<char, 1024, 2> >&, EList<Edit>&, int&, const char*, index_t, int, index_t, bool, EList<Edit>&, index_t, ELList<std::pair<_FIter, _FIter> >&, Haplotype<index_t>&, ELList<Edit, 128, 4>*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long 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:3556:58:   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) {
      |                        ~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from aligner_seed2.h:109,
                 from aligner_driver.h:78,
                 from hi_aligner.h:41,
                 from spliced_aligner.h:23,
                 from hisat2.cpp:46:
group_walk.h: In instantiation of ‘std::pair<int, int> GWState<index_t, T>::init(const GFM<index_t>&, const BitPairReference&, SARangeWithOffs<T, index_t>&, EList<GWState<index_t, T>, S>&, GWHit<index_t, T>&, index_t, bool, EList<WalkResult<index_t>, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice<short unsigned int, 16>]’:
group_walk.h:494:14:   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:3556:58:   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()) {
      |                    ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList<ALT<index_t> >&, const EList<Haplotype<index_t> >&, const EList<T>&, Haplotype<index_t>&, EList<std::pair<_FIter, _FIter> >&, index_t, bool, bool) [with index_t = long 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:3556:58:   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) {
      |                        ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
In file included from hisat2.cpp:46:
spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = long 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()) {
      |                        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from spliced_aligner.h:23,
                 from hisat2.cpp:46:
hi_aligner.h: In instantiation of ‘bool GenomeHit<index_t>::combineWith(const GenomeHit<index_t>&, const Read&, const GFM<index_t>&, const BitPairReference&, const ALTDB<index_t>&, const RepeatDB<index_t>&, SpliceSiteDB&, SwAligner&, SwMetrics&, const Scoring&, TAlScore, RandomSource&, index_t, index_t, index_t, index_t, index_t, index_t, const SpliceSite*, bool) [with index_t = long unsigned int; TAlScore = long int]’:
spliced_aligner.h:494:60:   required from ‘int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’
spliced_aligner.h:331:9:   required from here
hi_aligner.h:1926:32: warning: comparison of integer expressions of different signedness: ‘const uint64_t’ {aka ‘const long unsigned int’} and ‘char’ [-Wsign-compare]
 1926 |                     if(alt.seq == rdc) {
      |                        ~~~~~~~~^~~~~~
hi_aligner.h: In instantiation of ‘index_t HI_Aligner<index_t, local_index_t>::globalGFMSearch(const GFM<index_t>&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList<std::pair<_FIter, _FIter> >&, RandomSource&, bool&, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’:
spliced_aligner.h:1086:53:   required from ‘int64_t SplicedAligner<index_t, local_index_t>::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const ALTDB<index_t>&, const RepeatDB<index_t>&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit<index_t>&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’
spliced_aligner.h:331:9:   required from here
hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare]
 6719 |     if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) {
      |                                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from gfm.h:59,
                 from hgfm.h:24,
                 from hisat2.cpp:33:
repeat.h: In member function ‘int HI_Aligner<index_t, local_index_t>::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM<index_t>&, const GFM<index_t>*, const ALTDB<index_t>&, const RepeatDB<index_t>&, const ALTDB<index_t>&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap<index_t>&) [with index_t = long unsigned int; local_index_t = short unsigned int]’:
repeat.h:41:20: warning: ‘cmp.RepeatCoord<long unsigned int>::fw’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   41 |         if(fw != o.fw)
      |                  ~~^~
repeat.h:43:26: warning: ‘cmp.RepeatCoord<long unsigned int>::alleleID’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   43 |         if(alleleID != o.alleleID)
      |                        ~~^~~~~~~~
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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |   uint64_t origBufOff = bufOff;
      |            ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |  bool binarySearched = false;
      |       ^~~~~~~~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_seed.h:30,
                 from aligner_seed.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_seed2.cpp:22:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_seed2.cpp:22:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from aligner_result.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from aligner_result.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from aln_sink.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from aln_sink.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from unique.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from unique.h:38,
                 from unique.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_seed2.h:102,
                 from aligner_driver.h:78,
                 from aligner_driver.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from splice_site.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from splice_site.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from splice_site.cpp:20:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from splice_site.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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,
                 from splice_site.cpp:20:
ds.h: In instantiation of ‘void EList<T, S>::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’:
splice_site.cpp:722:59:   required from here
ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  663 |   std::memcpy(list_ + cur_, l, bytes);
      |   ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
In file included from edit.h:30,
                 from splice_site.cpp:20:
splice_site.h:377:7: note: ‘class Exon’ declared here
  377 | class Exon {
      |       ^~~~
x86_64-linux-gnu-g++ -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \
-DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"28 September 2021\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \
-I. -I third_party  -I . \
-o hisat2-inspect-s hisat2_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
In file included from hisat2_inspect.cpp:25:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
  227 |  if(!((a) <= (b))) { \
      |       ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
  180 |             assert_leq(fw, 1);
      |             ^~~~~~~~~~
In file included from hgfm.h:24,
                 from hisat2_inspect.cpp:27:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2_inspect.cpp:27:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hgfm.h:24,
                 from hisat2_inspect.cpp:27:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2_inspect.cpp:27:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
  227 |  if(!((a) <= (b))) { \
      |       ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
  180 |             assert_leq(fw, 1);
      |             ^~~~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
  227 |  if(!((a) <= (b))) { \
      |       ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
  180 |             assert_leq(fw, 1);
      |             ^~~~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
x86_64-linux-gnu-g++ -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \
-DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"28 September 2021\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \
-I. -I third_party  -I . \
-o hisat2-inspect-l hisat2_inspect.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
In file included from hisat2_inspect.cpp:25:
alt.h: In member function ‘bool ALT<index_t>::repOk() const’:
assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
  227 |  if(!((a) <= (b))) { \
      |       ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
  180 |             assert_leq(fw, 1);
      |             ^~~~~~~~~~
In file included from hgfm.h:24,
                 from hisat2_inspect.cpp:27:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2_inspect.cpp:27:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hgfm.h:24,
                 from hisat2_inspect.cpp:27:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from hgfm.h:24,
                 from hisat2_inspect.cpp:27:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
  227 |  if(!((a) <= (b))) { \
      |       ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
  180 |             assert_leq(fw, 1);
      |             ^~~~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare]
  227 |  if(!((a) <= (b))) { \
      |       ~~~~^~~~~~
alt.h:180:13: note: in expansion of macro ‘assert_leq’
  180 |             assert_leq(fw, 1);
      |             ^~~~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
x86_64-linux-gnu-g++ -O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3   -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \
-fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"28 September 2021\"" -DCOMPILER_VERSION="\"`x86_64-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DBOWTIE_MM  -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
-I. -I third_party  \
-o hisat2-repeat hisat2_repeat.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \
-lpthread  -Wl,-z,relro -Wl,-z,now
In file included from hisat2_repeat.cpp:36:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from hisat2_repeat.cpp:31:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from hisat2_repeat.cpp:36:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from hisat2_repeat.cpp:31:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from edit.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from edit.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from gfm.cpp:21:
gfm.h:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/memory:83,
                 from gfm.h:28,
                 from gfm.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’:
reference.cpp:522:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable]
  522 |   uint64_t origBufOff = bufOff;
      |            ^~~~~~~~~~
reference.cpp:516:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable]
  516 |  bool binarySearched = false;
      |       ^~~~~~~~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_bt.h:25,
                 from aligner_bt.cpp:20:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from aligner_result.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from aligner_result.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_sw.cpp:25:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_ee_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_i16.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_sw.h:75,
                 from aligner_swsse_loc_u8.cpp:56:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
In file included from splice_site.h:34,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
gfm.h: In static member function ‘static std::pair<GFM<index_t>*, GFM<index_t>*> GFM<index_t>::fromStrings(const EList<std::__cxx11::basic_string<char> >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from reference.h:36,
                 from splice_site.h:32,
                 from edit.h:30,
                 from aligner_result.h:30,
                 from aligner_sw_common.h:23,
                 from aligner_swsse.cpp:21:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from bit_packed_array.cpp:23:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from bit_packed_array.cpp:23:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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 string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’:
gfm.h:1185:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1185 |   auto_ptr<stringstream> ss(new stringstream());
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from repeat_builder.cpp:25:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   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:1189:3: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 1189 |   auto_ptr<FileBuf> fb(new FileBuf(ss.get()));
      |   ^~~~~~~~
In file included from /usr/x86_64-linux-gnu/include/c++/10/bits/locale_conv.h:41,
                 from /usr/x86_64-linux-gnu/include/c++/10/locale:43,
                 from /usr/x86_64-linux-gnu/include/c++/10/iomanip:43,
                 from timer.h:26,
                 from repeat_builder.cpp:25:
/usr/x86_64-linux-gnu/include/c++/10/bits/unique_ptr.h:57:28: note: declared here
   57 |   template<typename> class auto_ptr;
      |                            ^~~~~~~~
repeat_builder.cpp: In function ‘std::string reverse_complement(const string&)’:
repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts]
   88 |         rev[i] = asc2dnacomp[nt];
      |                              ^~
repeat_builder.cpp: In function ‘std::string reverseComplement(const string&)’:
repeat_builder.cpp:200:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  200 |   rc.push_back(asc2dnacomp[str[si - 1]]);
      |                                       ^
repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’:
repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘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 string&, size_t, size_t)’:
repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1217 |         kmer = (kmer << 2) | asc2dna[seq[offset + i]];
      |                                                     ^
repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’:
repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 1225 |     kmer = (kmer << 2) | asc2dna[base];
      |                                  ^~~~
repeat_builder.cpp: In function ‘void find_gap_pos(const string&, const string&, EList<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 string&, const string&, std::string&, size_t)’:
repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2915 |         pad[i] = "CGTA"[asc2dna[ref[i]]];
      |                                       ^
repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts]
 2919 |             pad[i] = "CGTA"[asc2dna[pad[i]]];
      |                                           ^
repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘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 string&, const string&, EList<Edit>&, Coord&)’:
repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable]
 3065 |         int max_match_len = 0;
      |             ^~~~~~~~~~~~~
In file included from repeat_builder.cpp:31:
repeat_builder.cpp: In instantiation of ‘RepeatBuilder<TStr>::RepeatBuilder(TStr&, const EList<RefRecord>&, const EList<std::__cxx11::basic_string<char> >&, bool, const string&) [with TStr = SString<char>; std::string = std::__cxx11::basic_string<char>]’:
repeat_builder.cpp:4753:16:   required from here
repeat_builder.h:947:17: warning: ‘RepeatBuilder<SString<char> >::coordHelper_’ will be initialized after [-Wreorder]
  947 |     CoordHelper coordHelper_;
      |                 ^~~~~~~~~~~~
repeat_builder.h:940:10: warning:   ‘bool RepeatBuilder<SString<char> >::forward_only_’ [-Wreorder]
  940 |     bool forward_only_;
      |          ^~~~~~~~~~~~~
repeat_builder.cpp:3167:1: warning:   when initialized here [-Wreorder]
 3167 | RepeatBuilder<TStr>::RepeatBuilder(TStr& s,
      | ^~~~~~~~~~~~~~~~~~~
repeat_builder.cpp: In instantiation of ‘void RepeatBuilder<TStr>::build(const RepeatParameter&) [with TStr = SString<char>]’:
repeat_builder.cpp:4753:16:   required from here
repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const 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 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 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 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 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:309:24: 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:310:25: 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:272:19: warning: array subscript has type ‘char’ [-Wchar-subscripts]
  272 |   char nt = "ACGT"[ref[start + i]];
      |             ~~~~~~^
repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString<char>; TIndexOffU = long 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]];
      |                   ~~~~~~^
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 2021-10-08T22:16:02Z

Finished
--------


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

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

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

Build Architecture: arm64
Build Profiles: cross nocheck
Build Type: any
Build-Space: 94184
Build-Time: 1695
Distribution: unstable
Fail-Stage: build
Foreign Architectures: amd64
Host Architecture: amd64
Install-Time: 72
Job: hisat2_2.2.1-3
Machine Architecture: arm64
Package: hisat2
Package-Time: 1797
Source-Version: 2.2.1-3
Space: 94184
Status: attempted
Version: 2.2.1-3
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Finished at 2021-10-08T22:16:02Z
Build needed 00:29:57, 94184k disk space