libvcflib →
1.0.3+dfsg-2 →
armhf → 2022-10-10 05:46:39
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| libvcflib 1.0.3+dfsg-2 (armhf) Mon, 10 Oct 2022 05:35:56 +0000 |
+==============================================================================+
Package: libvcflib
Version: 1.0.3+dfsg-2
Source Version: 1.0.3+dfsg-2
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-9b19ab73-d367-40ae-a7f6-69d00fcdf32e' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [13.4 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [14.2 MB]
Fetched 27.6 MB in 10s (2839 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
W: http://172.17.4.1/private/dists/bookworm-staging/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'libvcflib' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/libvcflib.git
Please use:
git clone https://salsa.debian.org/med-team/libvcflib.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 7567 kB of source archives.
Get:1 http://172.17.4.1/private bookworm-staging/main libvcflib 1.0.3+dfsg-2 (dsc) [2301 B]
Get:2 http://172.17.4.1/private bookworm-staging/main libvcflib 1.0.3+dfsg-2 (tar) [7556 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main libvcflib 1.0.3+dfsg-2 (diff) [8100 B]
Fetched 7567 kB in 1s (9118 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/libvcflib-RTIoWg/libvcflib-1.0.3+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libvcflib-RTIoWg' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-BtmC5T/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-BtmC5T/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-BtmC5T/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ Packages [433 B]
Fetched 2109 B in 0s (8007 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 3 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (69.3 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12808 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper-compat (= 13), cmake, markdown, libtabixpp-dev, libbz2-dev, libdisorder-dev, libsmithwaterman-dev, libssw-dev, libfastahack-dev, pkg-config, libgtest-dev, debhelper
Filtered Build-Depends: debhelper-compat (= 13), cmake, markdown, libtabixpp-dev, libbz2-dev, libdisorder-dev, libsmithwaterman-dev, libssw-dev, libfastahack-dev, pkg-config, libgtest-dev, debhelper
dpkg-deb: building package 'sbuild-build-depends-libvcflib-dummy' in '/<<BUILDDIR>>/resolver-BtmC5T/apt_archive/sbuild-build-depends-libvcflib-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-libvcflib-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ Sources [584 B]
Get:5 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ Packages [651 B]
Fetched 2568 B in 0s (12.0 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install libvcflib build dependencies (apt-based resolver)
---------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
krb5-locales libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file gettext gettext-base googletest groff-base
intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbz2-dev
libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1
libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libglib2.0-0
libgtest-dev libhts-dev libhts3 libhtscodecs2 libicu71 libjsoncpp25
liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1
libprocps8 libpsl5 librhash0 librtmp1 libsmithwaterman-dev libsmithwaterman0
libssh2-1 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0
libtool libuchardet0 libuv1 libxml2 m4 man-db markdown pkg-config po-debconf
procps zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build
cmake-format dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
lrzip libcurl4-doc libgnutls28-dev libidn11-dev libkrb5-dev libldap2-dev
librtmp-dev libssh2-1-dev liblzma-doc libtool-doc gfortran
| fortran95-compiler gcj-jdk m4-doc apparmor less www-browser
libmail-box-perl
Recommended packages:
curl | wget | lynx bzip2-doc ca-certificates libarchive-cpio-perl
libglib2.0-data shared-mime-info xdg-user-dirs libgpm2 publicsuffix
libltdl-dev libmail-sendmail-perl psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cmake cmake-data
debhelper dh-autoreconf dh-elpa-helper dh-strip-nondeterminism dwz
emacsen-common file gettext gettext-base googletest groff-base
intltool-debian libarchive-zip-perl libarchive13 libbrotli1 libbz2-dev
libcurl3-gnutls libcurl4 libcurl4-gnutls-dev libdebhelper-perl
libdeflate-dev libdeflate0 libdisorder-dev libdisorder0 libelf1 libexpat1
libfastahack-dev libfastahack0 libfile-stripnondeterminism-perl libglib2.0-0
libgtest-dev libhts-dev libhts3 libhtscodecs2 libicu71 libjsoncpp25
liblzma-dev libmagic-mgc libmagic1 libncurses6 libnghttp2-14 libpipeline1
libprocps8 libpsl5 librhash0 librtmp1 libsmithwaterman-dev libsmithwaterman0
libssh2-1 libssw-dev libssw0 libsub-override-perl libtabixpp-dev libtabixpp0
libtool libuchardet0 libuv1 libxml2 m4 man-db markdown pkg-config po-debconf
procps sbuild-build-depends-libvcflib-dummy zlib1g-dev
0 upgraded, 73 newly installed, 0 to remove and 3 not upgraded.
Need to get 31.6 MB of archives.
After this operation, 129 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-BtmC5T/apt_archive ./ sbuild-build-depends-libvcflib-dummy 0.invalid.0 [936 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.38.1-1 [137 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.6-3 [34.3 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.2-3 [1364 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libncurses6 armhf 6.3+20220423-2 [79.6 kB]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libprocps8 armhf 2:3.3.17-7 [60.7 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf procps armhf 2:3.3.17-7 [475 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-4 [295 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-4 [120 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-4 [65.8 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-9 [171 kB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.19-1 [260 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.3 [823 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-9 [510 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf libicu71 armhf 71.1-3 [8855 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.14+dfsg-1 [591 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libarchive13 armhf 3.6.0-1 [306 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b2 [260 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libnghttp2-14 armhf 1.50.0-1 [65.0 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libssh2-1 armhf 1.10.0-3+b1 [161 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf libcurl4 armhf 7.85.0-1 [325 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.9-1 [83.3 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libjsoncpp25 armhf 1.9.5-4 [66.7 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf librhash0 armhf 1.4.3-3 [142 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libuv1 armhf 1.44.2-1+rpi1 [125 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf dh-elpa-helper all 2.0.14 [11.5 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf emacsen-common all 3.0.4 [19.3 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf cmake-data all 3.24.2-1 [2019 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf cmake armhf 3.24.2-1 [3661 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.9.1 [196 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.7-4 [526 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-3 [10.4 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.187-2+rpi2 [177 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14+20220924-2 [93.1 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-9 [1220 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.9.1 [1071 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf googletest all 1.12.1-0.2 [506 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf libbz2-dev armhf 1.0.8-5+b2 [26.8 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libcurl3-gnutls armhf 7.85.0-1 [320 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libcurl4-gnutls-dev armhf 7.85.0-1 [397 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf libdeflate0 armhf 1.14-1 [50.9 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf libdeflate-dev armhf 1.14-1 [48.1 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-4 [4856 B]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-4 [4484 B]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf libfastahack0 armhf 1.0.0+dfsg-10 [23.9 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf libfastahack-dev armhf 1.0.0+dfsg-10 [26.3 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.74.0-2 [1265 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf libgtest-dev armhf 1.12.1-0.2 [230 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf libhtscodecs2 armhf 1.3.0-3 [59.5 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf libhts3 armhf 1.16+ds-2 [371 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf liblzma-dev armhf 5.2.5-2.1 [218 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-4.1 [183 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf libhts-dev armhf 1.16+ds-2 [1483 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-12 [32.4 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-12 [36.7 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libssw0 armhf 1.1-13 [21.0 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf libssw-dev armhf 1.1-13 [24.0 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf libtabixpp0 armhf 1.1.1-1 [8960 B]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libtabixpp-dev armhf 1.1.1-1 [8532 B]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf markdown all 1.0.1-10.1 [17.5 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
debconf: delaying package configuration, since apt-utils is not installed
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Setting up autotools-dev (20220109.1) ...
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Setting up emacsen-common (3.0.4) ...
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Setting up dh-elpa-helper (2.0.14) ...
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Setting up autopoint (0.21-9) ...
Setting up libjsoncpp25:armhf (1.9.5-4) ...
Setting up pkg-config (0.29.2-1) ...
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Setting up autoconf (2.71-2) ...
Setting up liblzma-dev:armhf (5.2.5-2.1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-4.1) ...
Setting up librhash0:armhf (1.4.3-3) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-3) ...
Setting up libssh2-1:armhf (1.10.0-3+b1) ...
Setting up cmake-data (3.24.2-1) ...
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Setting up libelf1:armhf (0.187-2+rpi2) ...
Setting up libssw0:armhf (1.1-13) ...
Setting up libxml2:armhf (2.9.14+dfsg-1) ...
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Setting up markdown (1.0.1-10.1) ...
Setting up libbz2-dev:armhf (1.0.8-5+b2) ...
Setting up automake (1:1.16.5-1.3) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up gettext (0.21-9) ...
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Setting up libtool (2.4.7-4) ...
Setting up libarchive13:armhf (3.6.0-1) ...
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Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14+20220924-2) ...
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Setting up po-debconf (1.0.21+nmu1) ...
Setting up libhts-dev:armhf (1.16+ds-2) ...
Setting up man-db (2.10.2-3) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libtabixpp0:armhf (1.1.1-1) ...
Setting up cmake (3.24.2-1) ...
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Setting up libtabixpp-dev:armhf (1.1.1-1) ...
Setting up sbuild-build-depends-libvcflib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.35-1+rpi2) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.15.0-187-generic armhf (armv8l)
Toolchain package versions: binutils_2.39-6+rpi1 dpkg-dev_1.21.9+rpi1 g++-12_12.2.0-3+rpi1 gcc-12_12.2.0-3+rpi1 libc6-dev_2.35-1+rpi2 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 linux-libc-dev_5.19.6-1+rpi1
Package versions: adduser_3.129 apt_2.5.3 autoconf_2.71-2 automake_1:1.16.5-1.3 autopoint_0.21-9 autotools-dev_20220109.1 base-files_12.2+rpi1 base-passwd_3.6.1 bash_5.2~rc2-2 binutils_2.39-6+rpi1 binutils-arm-linux-gnueabihf_2.39-6+rpi1 binutils-common_2.39-6+rpi1 bsdextrautils_2.38.1-1 bsdutils_1:2.38.1-1 build-essential_12.9 bzip2_1.0.8-5+b2 cmake_3.24.2-1 cmake-data_3.24.2-1 coreutils_9.1-1 cpp_4:12.2.0-1+rpi1 cpp-12_12.2.0-3+rpi1 dash_0.5.11+git20210903+057cd650a4ed-9 debconf_1.5.79 debhelper_13.9.1 debianutils_5.7-0.3 dh-autoreconf_20 dh-elpa-helper_2.0.14 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.8-1 dirmngr_2.2.39-1 dpkg_1.21.9+rpi1 dpkg-dev_1.21.9+rpi1 dwz_0.14+20220924-2 e2fsprogs_1.46.6~rc1-1 emacsen-common_3.0.4 fakeroot_1.29-1 file_1:5.41-4 findutils_4.9.0-3 g++_4:12.2.0-1+rpi1 g++-12_12.2.0-3+rpi1 gcc_4:12.2.0-1+rpi1 gcc-12_12.2.0-3+rpi1 gcc-12-base_12.2.0-3+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-9 gettext-base_0.21-9 gnupg_2.2.39-1 gnupg-l10n_2.2.39-1 gnupg-utils_2.2.39-1 googletest_1.12.1-0.2 gpg_2.2.39-1 gpg-agent_2.2.39-1 gpg-wks-client_2.2.39-1 gpg-wks-server_2.2.39-1 gpgconf_2.2.39-1 gpgsm_2.2.39-1 gpgv_2.2.39-1 grep_3.7-1 groff-base_1.22.4-8 gzip_1.12-1 hostname_3.23 init-system-helpers_1.64 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20211215-1 krb5-locales_1.20-1 libacl1_2.3.1-1 libapt-pkg6.0_2.5.3 libarchive-zip-perl_1.68-1 libarchive13_3.6.0-1 libasan8_12.2.0-3+rpi1 libassuan0_2.5.5-4 libatomic1_12.2.0-3+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.7-1.1 libaudit1_1:3.0.7-1.1 libbinutils_2.39-6+rpi1 libblkid1_2.38.1-1 libbrotli1_1.0.9-2+b2 libbz2-1.0_1.0.8-5+b2 libbz2-dev_1.0.8-5+b2 libc-bin_2.35-1+rpi2 libc-dev-bin_2.35-1+rpi2 libc6_2.35-1+rpi2 libc6-dev_2.35-1+rpi2 libcap-ng0_0.8.3-1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_12.2.0-3+rpi1 libcom-err2_1.46.6~rc1-1 libcrypt-dev_1:4.4.28-2 libcrypt1_1:4.4.28-2 libctf-nobfd0_2.39-6+rpi1 libctf0_2.39-6+rpi1 libcurl3-gnutls_7.85.0-1 libcurl4_7.85.0-1 libcurl4-gnutls-dev_7.85.0-1 libdb5.3_5.3.28+dfsg1-0.10 libdebconfclient0_0.264 libdebhelper-perl_13.9.1 libdeflate-dev_1.14-1 libdeflate0_1.14-1 libdisorder-dev_0.0.2+git20130809.8062ee1-4 libdisorder0_0.0.2+git20130809.8062ee1-4 libdpkg-perl_1.21.9+rpi1 libelf1_0.187-2+rpi2 libexpat1_2.4.9-1 libext2fs2_1.46.6~rc1-1 libfakeroot_1.29-1 libfastahack-dev_1.0.0+dfsg-10 libfastahack0_1.0.0+dfsg-10 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libgcc-12-dev_12.2.0-3+rpi1 libgcc-s1_12.2.0-3+rpi1 libgcrypt20_1.10.1-2+b2 libgdbm-compat4_1.23-2 libgdbm6_1.23-2 libglib2.0-0_2.74.0-2 libgmp10_2:6.2.1+dfsg1-1 libgnutls30_3.7.7-2 libgomp1_12.2.0-3+rpi1 libgpg-error0_1.45-2 libgssapi-krb5-2_1.20-1 libgtest-dev_1.12.1-0.2 libhogweed6_3.8.1-2 libhts-dev_1.16+ds-2 libhts3_1.16+ds-2 libhtscodecs2_1.3.0-3 libicu71_71.1-3 libidn2-0_2.3.3-1 libisl23_0.25-1 libjsoncpp25_1.9.5-4 libk5crypto3_1.20-1 libkeyutils1_1.6.3-1 libkrb5-3_1.20-1 libkrb5support0_1.20-1 libksba8_1.6.0-3 libldap-2.5-0_2.5.13+dfsg-2+rpi1 liblz4-1_1.9.4-1+rpi1 liblzma-dev_5.2.5-2.1 liblzma5_5.2.5-2.1 libmagic-mgc_1:5.41-4 libmagic1_1:5.41-4 libmount1_2.38.1-1 libmpc3_1.2.1-2 libmpfr6_4.1.0-3 libncurses6_6.3+20220423-2 libncursesw6_6.3+20220423-2 libnettle8_3.8.1-2 libnghttp2-14_1.50.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libp11-kit0_0.24.1-1 libpam-cap_1:2.44-1 libpam-modules_1.5.2-2 libpam-modules-bin_1.5.2-2 libpam-runtime_1.5.2-2 libpam0g_1.5.2-2 libpcre2-8-0_10.40-1+b2 libpcre3_2:8.39-14 libperl5.34_5.34.0-5 libpipeline1_1.5.6-3 libprocps8_2:3.3.17-7 libpsl5_0.21.0-1.2 libreadline8_8.2-1 librhash0_1.4.3-3 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 libsasl2-2_2.1.28+dfsg-8 libsasl2-modules-db_2.1.28+dfsg-8 libseccomp2_2.5.4-1+rpi1 libselinux1_3.4-1 libsemanage-common_3.4-1 libsemanage2_3.4-1 libsepol1_3.1-1 libsepol2_3.4-2 libsmartcols1_2.38.1-1 libsmithwaterman-dev_0.0+git20160702.2610e25-12 libsmithwaterman0_0.0+git20160702.2610e25-12 libsqlite3-0_3.39.4-1 libss2_1.46.6~rc1-1 libssh2-1_1.10.0-3+b1 libssl1.1_1.1.1o-1 libssl3_3.0.5-2 libssw-dev_1.1-13 libssw0_1.1-13 libstdc++-12-dev_12.2.0-3+rpi1 libstdc++6_12.2.0-3+rpi1 libsub-override-perl_0.09-3 libsystemd0_251.4-3+rpi1 libtabixpp-dev_1.1.1-1 libtabixpp0_1.1.1-1 libtasn1-6_4.19.0-2 libtinfo6_6.3+20220423-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-4 libubsan1_12.2.0-3+rpi1 libuchardet0_0.0.7-1 libudev1_251.4-3+rpi1 libunistring2_1.0-1 libuuid1_2.38.1-1 libuv1_1.44.2-1+rpi1 libxml2_2.9.14+dfsg-1 libxxhash0_0.8.1-1 libzstd1_1.5.2+dfsg-1 linux-libc-dev_5.19.6-1+rpi1 login_1:4.11.1+dfsg1-2 logsave_1.46.6~rc1-1 lsb-base_11.4+rpi1 m4_1.4.19-1 make_4.3-4.1 man-db_2.10.2-3 markdown_1.0.1-10.1 mawk_1.3.4.20200120-3.1 mount_2.38.1-1 nano_6.4-1 ncurses-base_6.3+20220423-2 ncurses-bin_6.3+20220423-2 netbase_6.3 passwd_1:4.11.1+dfsg1-2 patch_2.7.6-7 perl_5.34.0-5 perl-base_5.34.0-5 perl-modules-5.34_5.34.0-5 pinentry-curses_1.2.0-2 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 procps_2:3.3.17-7 raspbian-archive-keyring_20120528.2 readline-common_8.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libvcflib-dummy_0.invalid.0 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 sysvinit-utils_3.05-6 tar_1.34+dfsg-1 tzdata_2022d-1 util-linux_2.38.1-1 util-linux-extra_2.38.1-1 xz-utils_5.2.5-2.1 zlib1g_1:1.2.11.dfsg-4.1 zlib1g-dev_1:1.2.11.dfsg-4.1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.bpjCreRs/trustedkeys.kbx': General error
gpgv: Signature made Fri Oct 7 14:31:55 2022 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./libvcflib_1.0.3+dfsg-2.dsc
dpkg-source: info: extracting libvcflib in /<<BUILDDIR>>/libvcflib-1.0.3+dfsg
dpkg-source: info: unpacking libvcflib_1.0.3+dfsg.orig.tar.xz
dpkg-source: info: unpacking libvcflib_1.0.3+dfsg-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying no_fsom
dpkg-source: info: applying use_debian_packaged_smithwaterman.patch
dpkg-source: info: applying use_debian_packaged_fastahack.patch
dpkg-source: info: applying use_debian_packaged_libssw.patch
dpkg-source: info: applying shared_lib.patch
dpkg-source: info: applying pkg-config.patch
dpkg-source: info: applying tabix_linking
dpkg-source: info: applying tests
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-9b19ab73-d367-40ae-a7f6-69d00fcdf32e
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package libvcflib
dpkg-buildpackage: info: source version 1.0.3+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh clean --buildsystem cmake
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_auto_clean || true
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_autoreconf_clean -O--buildsystem=cmake
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_clean
find . -name "*.o" -delete
rm -f README.html
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
debian/rules binary-arch
dh binary-arch --buildsystem cmake
dh_update_autotools_config -a -O--buildsystem=cmake
dh_autoreconf -a -O--buildsystem=cmake
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_auto_configure -- -DOPENMP=ON -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON
cd obj-arm-linux-gnueabihf && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/arm-linux-gnueabihf -DOPENMP=ON -DCMAKE_BUILD_RPATH_USE_ORIGIN=ON ..
-- The C compiler identification is GNU 12.2.0
-- The CXX compiler identification is GNU 12.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.2")
-- Found BZip2: /usr/lib/arm-linux-gnueabihf/libbz2.so (found version "1.0.8")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Looking for lzma_auto_decoder in /usr/lib/arm-linux-gnueabihf/liblzma.so
-- Looking for lzma_auto_decoder in /usr/lib/arm-linux-gnueabihf/liblzma.so - found
-- Looking for lzma_easy_encoder in /usr/lib/arm-linux-gnueabihf/liblzma.so
-- Looking for lzma_easy_encoder in /usr/lib/arm-linux-gnueabihf/liblzma.so - found
-- Looking for lzma_lzma_preset in /usr/lib/arm-linux-gnueabihf/liblzma.so
-- Looking for lzma_lzma_preset in /usr/lib/arm-linux-gnueabihf/liblzma.so - found
-- Found LibLZMA: /usr/lib/arm-linux-gnueabihf/liblzma.so (found version "5.2.5")
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
--
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Checking for module 'htslib'
-- Found htslib, version 1.16
-- Checking for module 'tabixpp'
-- No package 'tabixpp' found
-- Checking for module 'libsmithwaterman'
-- Found libsmithwaterman, version 0.0
-- Checking for module 'libfastahack'
-- Found libfastahack, version 0.0
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
Pandoc needs to be installed to generate the man pages
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_EXPORT_NO_PACKAGE_REGISTRY
CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY
CMAKE_INSTALL_LOCALSTATEDIR
CMAKE_INSTALL_RUNSTATEDIR
CMAKE_INSTALL_SYSCONFDIR
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_auto_build
cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1
make[2]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/libvcflib-1.0.3+dfsg -B/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[3]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflib.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 1%] Building CXX object CMakeFiles/vcflib.dir/src/rnglib.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/rnglib.cpp.o -MF CMakeFiles/vcflib.dir/src/rnglib.cpp.o.d -o CMakeFiles/vcflib.dir/src/rnglib.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/rnglib.cpp
[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/var.cpp.o
[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/pdflib.cpp.o
[ 2%] Building CXX object CMakeFiles/vcflib.dir/src/Variant.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/var.cpp.o -MF CMakeFiles/vcflib.dir/src/var.cpp.o.d -o CMakeFiles/vcflib.dir/src/var.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/pdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/pdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/pdflib.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pdflib.cpp
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/Variant.cpp.o -MF CMakeFiles/vcflib.dir/src/Variant.cpp.o.d -o CMakeFiles/vcflib.dir/src/Variant.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.cpp
[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/cdflib.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/cdflib.cpp.o -MF CMakeFiles/vcflib.dir/src/cdflib.cpp.o.d -o CMakeFiles/vcflib.dir/src/cdflib.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/cdflib.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.hpp:17,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:20:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
[ 3%] Building CXX object CMakeFiles/vcflib.dir/src/split.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -Dvcflib_EXPORTS -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -fPIC -MD -MT CMakeFiles/vcflib.dir/src/split.cpp.o -MF CMakeFiles/vcflib.dir/src/split.cpp.o.d -o CMakeFiles/vcflib.dir/src/split.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/split.cpp
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:286:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:287:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:288:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:293:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:296:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:300:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:303:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:304:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:305:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:306:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:307:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:308:26:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'virtual void pooled::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:185:18:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void pooled::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:187:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'virtual void pooled::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/var.cpp:188:20:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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[ 6%] Building CXX object CMakeFiles/bFst.dir/src/bFst.cpp.o
[ 6%] Building CXX object CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -MF CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o.d -o CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/bFst.dir/src/bFst.cpp.o -MF CMakeFiles/bFst.dir/src/bFst.cpp.o.d -o CMakeFiles/bFst.dir/src/bFst.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/dumpContigsFromHeader.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfecho.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pVst.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 7%] Linking CXX executable dumpContigsFromHeader
/usr/bin/cmake -E cmake_link_script CMakeFiles/dumpContigsFromHeader.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/dumpContigsFromHeader.dir/src/dumpContigsFromHeader.cpp.o -o dumpContigsFromHeader -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 7%] Built target dumpContigsFromHeader
make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/hapLrt.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/hapLrt.dir/build.make CMakeFiles/hapLrt.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 8%] Building CXX object CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -MF CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o.d -o CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/hapLrt.cpp
[ 8%] Linking CXX executable vcfecho
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfecho.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfecho.dir/src/vcfecho.cpp.o -o vcfecho -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 8%] Built target vcfecho
make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/popStats.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/popStats.dir/build.make CMakeFiles/popStats.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 9%] Building CXX object CMakeFiles/popStats.dir/src/popStats.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/popStats.dir/src/popStats.cpp.o -MF CMakeFiles/popStats.dir/src/popStats.cpp.o.d -o CMakeFiles/popStats.dir/src/popStats.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/popStats.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void phardy(std::vector<double>&, double, double)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp:179:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void phardy(std::vector<double>&, double, double)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp:180:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void phardy(std::vector<double>&, double, double)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp:181:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void calc(copyNcounts*)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pVst.cpp:203:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void calc(copyNcounts*)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pVst.cpp:206:25:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/popStats.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, pop&)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp:73:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, pop&)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp:74:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, pop&)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp:75:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void loadDat(copyNcounts*, std::string&, std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pVst.cpp:265:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void loadDat(copyNcounts*, std::string&, std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pVst.cpp:266:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void loadDat(copyNcounts*, std::string&, std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pVst.cpp:274:28:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'void loadDat(copyNcounts*, std::string&, std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pVst.cpp:275:23:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/bFst.cpp:583:22:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 10%] Linking CXX executable bFst
/usr/bin/cmake -E cmake_link_script CMakeFiles/bFst.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/bFst.dir/src/bFst.cpp.o -o bFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 10%] Built target bFst
make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/wcFst.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/wcFst.dir/build.make CMakeFiles/wcFst.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 11%] Building CXX object CMakeFiles/wcFst.dir/src/wcFst.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/wcFst.dir/src/wcFst.cpp.o -MF CMakeFiles/wcFst.dir/src/wcFst.cpp.o.d -o CMakeFiles/wcFst.dir/src/wcFst.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/wcFst.cpp
[ 12%] Linking CXX executable pVst
/usr/bin/cmake -E cmake_link_script CMakeFiles/pVst.dir/link.txt --verbose=1
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pVst.dir/src/pVst.cpp.o -o pVst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 12%] Built target pVst
make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/iHS.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/iHS.dir/build.make CMakeFiles/iHS.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 13%] Building CXX object CMakeFiles/iHS.dir/src/iHS.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/iHS.dir/src/iHS.cpp.o -MF CMakeFiles/iHS.dir/src/iHS.cpp.o.d -o CMakeFiles/iHS.dir/src/iHS.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/iHS.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/hapLrt.cpp:609:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/wcFst.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/iHS.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 14%] Linking CXX executable popStats
/usr/bin/cmake -E cmake_link_script CMakeFiles/popStats.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/popStats.dir/src/popStats.cpp.o -o popStats -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 14%] Built target popStats
make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/segmentFst.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/segmentFst.dir/build.make CMakeFiles/segmentFst.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 14%] Building CXX object CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -MF CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o.d -o CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/segmentFst.cpp
In file included from /usr/include/c++/12/map:60,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:15:
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 14%] Linking CXX executable hapLrt
/usr/bin/cmake -E cmake_link_script CMakeFiles/hapLrt.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/hapLrt.dir/src/hapLrt.cpp.o -o hapLrt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 14%] Built target hapLrt
make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/segmentIhs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/segmentIhs.dir/build.make CMakeFiles/segmentIhs.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 14%] Building CXX object CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -MF CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o.d -o CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/segmentIhs.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/split.h:15,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/segmentFst.cpp:59:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/segmentFst.cpp:294:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'bool gDist(int, int, double*)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/iHS.cpp:106:40:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'bool gDist(int, int, double*)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/iHS.cpp:106:69:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[ 15%] Linking CXX executable segmentFst
/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentFst.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentFst.dir/src/segmentFst.cpp.o -o segmentFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'void loadGeneticMap(int, int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/iHS.cpp:151:25:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 15%] Built target segmentFst
make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/genotypeSummary.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/genotypeSummary.dir/build.make CMakeFiles/genotypeSummary.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 16%] Building CXX object CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -MF CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o.d -o CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/genotypeSummary.cpp
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/split.h:15,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/segmentIhs.cpp:59:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/segmentIhs.cpp:291:21:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 17%] Linking CXX executable segmentIhs
/usr/bin/cmake -E cmake_link_script CMakeFiles/segmentIhs.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/segmentIhs.dir/src/segmentIhs.cpp.o -o segmentIhs -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/genotypeSummary.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/iHS.cpp:648:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 17%] Built target segmentIhs
make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/sequenceDiversity.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/sequenceDiversity.dir/build.make CMakeFiles/sequenceDiversity.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 17%] Building CXX object CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -MF CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o.d -o CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp
[ 18%] Linking CXX executable wcFst
/usr/bin/cmake -E cmake_link_script CMakeFiles/wcFst.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/wcFst.dir/src/wcFst.cpp.o -o wcFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 18%] Built target wcFst
make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/pFst.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/pFst.dir/build.make CMakeFiles/pFst.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 18%] Building CXX object CMakeFiles/pFst.dir/src/pFst.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/pFst.dir/src/pFst.cpp.o -MF CMakeFiles/pFst.dir/src/pFst.cpp.o.d -o CMakeFiles/pFst.dir/src/pFst.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pFst.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/sequenceDiversity.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/pFst.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 18%] Linking CXX executable iHS
/usr/bin/cmake -E cmake_link_script CMakeFiles/iHS.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/iHS.dir/src/iHS.cpp.o -o iHS -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 18%] Built target iHS
make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/smoother.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/smoother.dir/build.make CMakeFiles/smoother.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 19%] Building CXX object CMakeFiles/smoother.dir/src/smoother.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/smoother.dir/src/smoother.cpp.o -MF CMakeFiles/smoother.dir/src/smoother.cpp.o.d -o CMakeFiles/smoother.dir/src/smoother.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/smoother.cpp
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 19%] Linking CXX executable genotypeSummary
/usr/bin/cmake -E cmake_link_script CMakeFiles/genotypeSummary.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/genotypeSummary.dir/src/genotypeSummary.cpp.o -o genotypeSummary -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
[ 19%] Linking CXX executable smoother
/usr/bin/cmake -E cmake_link_script CMakeFiles/smoother.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/smoother.dir/src/smoother.cpp.o -o smoother -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 19%] Built target genotypeSummary
make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfld.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfld.dir/build.make CMakeFiles/vcfld.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 20%] Building CXX object CMakeFiles/vcfld.dir/src/vcfld.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfld.dir/src/vcfld.cpp.o -MF CMakeFiles/vcfld.dir/src/vcfld.cpp.o.d -o CMakeFiles/vcfld.dir/src/vcfld.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfld.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 20%] Built target smoother
make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/plotHaps.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/plotHaps.dir/build.make CMakeFiles/plotHaps.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 21%] Building CXX object CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -MF CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o.d -o CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/plotHaps.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfld.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 22%] Linking CXX executable pFst
/usr/bin/cmake -E cmake_link_script CMakeFiles/pFst.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/pFst.dir/src/pFst.cpp.o -o pFst -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
[ 23%] Linking CXX executable sequenceDiversity
/usr/bin/cmake -E cmake_link_script CMakeFiles/sequenceDiversity.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/sequenceDiversity.dir/src/sequenceDiversity.cpp.o -o sequenceDiversity -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 23%] Built target pFst
make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/abba-baba.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/abba-baba.dir/build.make CMakeFiles/abba-baba.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 23%] Building CXX object CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -MF CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o.d -o CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/abba-baba.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 23%] Built target sequenceDiversity
make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteGPAT++.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/permuteGPAT++.dir/build.make CMakeFiles/permuteGPAT++.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 24%] Building CXX object CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -MF CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o.d -o CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/split.h:15,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp:49:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/abba-baba.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/permuteGPAT++.cpp:184:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 24%] Linking CXX executable permuteGPAT++
/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteGPAT++.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteGPAT++.dir/src/permuteGPAT++.cpp.o -o permuteGPAT++ -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 24%] Built target permuteGPAT++
make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/permuteSmooth.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/permuteSmooth.dir/build.make CMakeFiles/permuteSmooth.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 25%] Building CXX object CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -MF CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o.d -o CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/plotHaps.cpp:375:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/split.h:15,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp:49:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'bool getContiguousWindow(std::vector<score*>&, std::vector<double>&, int, int*)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/permuteSmooth.cpp:249:19:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 25%] Linking CXX executable permuteSmooth
/usr/bin/cmake -E cmake_link_script CMakeFiles/permuteSmooth.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/permuteSmooth.dir/src/permuteSmooth.cpp.o -o permuteSmooth -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 25%] Built target permuteSmooth
make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/normalize-iHS.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/normalize-iHS.dir/build.make CMakeFiles/normalize-iHS.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 25%] Building CXX object CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -MF CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o.d -o CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp
[ 25%] Linking CXX executable plotHaps
/usr/bin/cmake -E cmake_link_script CMakeFiles/plotHaps.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/plotHaps.dir/src/plotHaps.cpp.o -o plotHaps -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 25%] Built target plotHaps
make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/meltEHH.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/meltEHH.dir/build.make CMakeFiles/meltEHH.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 26%] Building CXX object CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -MF CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o.d -o CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/meltEHH.cpp
[ 27%] Linking CXX executable vcfld
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfld.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfld.dir/src/vcfld.cpp.o -o vcfld -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 27%] Built target vcfld
make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaltcount.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfaltcount.dir/build.make CMakeFiles/vcfaltcount.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 28%] Building CXX object CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -MF CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o.d -o CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp
[ 29%] Linking CXX executable abba-baba
/usr/bin/cmake -E cmake_link_script CMakeFiles/abba-baba.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/abba-baba.dir/src/abba-baba.cpp.o" -o abba-baba -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 29%] Built target abba-baba
make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhetcount.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfhetcount.dir/build.make CMakeFiles/vcfhetcount.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 30%] Building CXX object CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -MF CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o.d -o CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp
In file included from /usr/include/c++/12/vector:70,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/split.h:15,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp:59:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void normalize(std::vector<iHSdat*>&, int*)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/normalize-iHS.cpp:229:21:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfaltcount.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 31%] Linking CXX executable normalize-iHS
/usr/bin/cmake -E cmake_link_script CMakeFiles/normalize-iHS.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic "CMakeFiles/normalize-iHS.dir/src/normalize-iHS.cpp.o" -o normalize-iHS -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 31%] Built target normalize-iHS
make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfhethomratio.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfhethomratio.dir/build.make CMakeFiles/vcfhethomratio.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 32%] Building CXX object CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -MF CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o.d -o CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfhetcount.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:15:
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, double>; _KeyOfValue = std::_Select1st<std::pair<const int, double> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfhethomratio.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 32%] Linking CXX executable vcfaltcount
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaltcount.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaltcount.dir/src/vcfaltcount.cpp.o -o vcfaltcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 32%] Built target vcfaltcount
make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffilter.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcffilter.dir/build.make CMakeFiles/vcffilter.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 33%] Building CXX object CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -MF CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o.d -o CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcffilter.cpp
In file included from /usr/include/c++/12/map:61:
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'bool gDist(int, int, double*)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:105:40:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'bool gDist(int, int, double*)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:105:69:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, double> >]',
inlined from 'void loadGeneticMap(int, int)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:150:25:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, double>, std::_Select1st<std::pair<const int, double> >, std::less<int>, std::allocator<std::pair<const int, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcffilter.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 33%] Linking CXX executable vcfhetcount
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhetcount.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhetcount.dir/src/vcfhetcount.cpp.o -o vcfhetcount -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 33%] Built target vcfhetcount
make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2tsv.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcf2tsv.dir/build.make CMakeFiles/vcf2tsv.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 34%] Building CXX object CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -MF CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o.d -o CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/meltEHH.cpp:636:20:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 34%] Linking CXX executable vcfhethomratio
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfhethomratio.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfhethomratio.dir/src/vcfhethomratio.cpp.o -o vcfhethomratio -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcf2tsv.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 34%] Built target vcfhethomratio
make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypes.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfgenotypes.dir/build.make CMakeFiles/vcfgenotypes.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 34%] Building CXX object CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -MF CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o.d -o CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgenotypes.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 35%] Linking CXX executable meltEHH
/usr/bin/cmake -E cmake_link_script CMakeFiles/meltEHH.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/meltEHH.dir/src/meltEHH.cpp.o -o meltEHH -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 35%] Built target meltEHH
make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotategenotypes.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfannotategenotypes.dir/build.make CMakeFiles/vcfannotategenotypes.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 36%] Building CXX object CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -MF CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o.d -o CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 37%] Linking CXX executable vcf2tsv
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2tsv.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2tsv.dir/src/vcf2tsv.cpp.o -o vcf2tsv -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
[ 38%] Linking CXX executable vcfgenotypes
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypes.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypes.dir/src/vcfgenotypes.cpp.o -o vcfgenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 38%] Built target vcf2tsv
make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcommonsamples.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfcommonsamples.dir/build.make CMakeFiles/vcfcommonsamples.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 39%] Building CXX object CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -MF CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o.d -o CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 39%] Built target vcfgenotypes
make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremovesamples.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfremovesamples.dir/build.make CMakeFiles/vcfremovesamples.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 39%] Building CXX object CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -MF CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o.d -o CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfremovesamples.cpp
[ 40%] Linking CXX executable vcffilter
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffilter.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffilter.dir/src/vcffilter.cpp.o -o vcffilter -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 40%] Built target vcffilter
make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepsamples.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfkeepsamples.dir/build.make CMakeFiles/vcfkeepsamples.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 41%] Building CXX object CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -MF CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o.d -o CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcommonsamples.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfremovesamples.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfkeepsamples.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 42%] Linking CXX executable vcfcommonsamples
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcommonsamples.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcommonsamples.dir/src/vcfcommonsamples.cpp.o -o vcfcommonsamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 42%] Built target vcfcommonsamples
make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplenames.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfsamplenames.dir/build.make CMakeFiles/vcfsamplenames.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 43%] Building CXX object CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -MF CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o.d -o CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp
[ 44%] Linking CXX executable vcfremovesamples
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremovesamples.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremovesamples.dir/src/vcfremovesamples.cpp.o -o vcfremovesamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 44%] Built target vcfremovesamples
make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenotypecompare.dir/DependInfo.cmake --color=
[ 44%] Linking CXX executable vcfkeepsamples
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepsamples.dir/link.txt --verbose=1
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepsamples.dir/src/vcfkeepsamples.cpp.o -o vcfkeepsamples -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make -f CMakeFiles/vcfgenotypecompare.dir/build.make CMakeFiles/vcfgenotypecompare.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 44%] Building CXX object CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -MF CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o.d -o CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 44%] Built target vcfkeepsamples
make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/depend
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cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcffixup.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcffixup.dir/build.make CMakeFiles/vcffixup.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 44%] Building CXX object CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -MF CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o.d -o CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcffixup.cpp
In file included from /usr/include/c++/12/map:60,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:15:
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >&&>, std::tuple<>}; _Key = std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >; _Val = std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant>; _KeyOfValue = std::_Select1st<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >; _Compare = std::less<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; _Alloc = std::allocator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant>, std::_Select1st<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >, std::less<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >; _Tp = vcflib::Variant; _Compare = std::less<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; _Alloc = std::allocator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >]':
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant>, std::_Select1st<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >, std::less<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsamplenames.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgenotypecompare.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcffixup.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
[ 45%] Linking CXX executable vcfsamplenames
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplenames.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplenames.dir/src/vcfsamplenames.cpp.o -o vcfsamplenames -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 45%] Built target vcfsamplenames
make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfclassify.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfclassify.dir/build.make CMakeFiles/vcfclassify.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 46%] Building CXX object CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -MF CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o.d -o CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:202:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:201:28:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >; _Tp = vcflib::Variant; _Compare = std::less<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; _Alloc = std::allocator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:215:62:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant>, std::_Select1st<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >, std::less<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >; _Tp = vcflib::Variant; _Compare = std::less<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >; _Alloc = std::allocator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfannotategenotypes.cpp:218:62:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant>, std::_Select1st<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >, std::less<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >, std::allocator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfclassify.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 47%] Linking CXX executable vcffixup
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcffixup.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcffixup.dir/src/vcffixup.cpp.o -o vcffixup -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 47%] Built target vcffixup
make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsamplediff.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfsamplediff.dir/build.make CMakeFiles/vcfsamplediff.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 48%] Building CXX object CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -MF CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o.d -o CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp
[ 49%] Linking CXX executable vcfannotategenotypes
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotategenotypes.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotategenotypes.dir/src/vcfannotategenotypes.cpp.o -o vcfannotategenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 49%] Built target vcfannotategenotypes
make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremoveaberrantgenotypes.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfremoveaberrantgenotypes.dir/build.make CMakeFiles/vcfremoveaberrantgenotypes.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 49%] Building CXX object CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -MF CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o.d -o CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsamplediff.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 49%] Linking CXX executable vcfclassify
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfclassify.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfclassify.dir/src/vcfclassify.cpp.o -o vcfclassify -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 49%] Built target vcfclassify
make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandom.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfrandom.dir/build.make CMakeFiles/vcfrandom.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 50%] Building CXX object CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -MF CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o.d -o CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfremoveaberrantgenotypes.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp:13:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/string:48,
from /usr/include/c++/12/bits/locale_classes.h:40,
from /usr/include/c++/12/bits/ios_base.h:41,
from /usr/include/c++/12/ios:42,
from /usr/include/c++/12/istream:38,
from /usr/include/c++/12/sstream:38,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfrandom.cpp:10:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 51%] Linking CXX executable vcfgenotypecompare
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenotypecompare.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenotypecompare.dir/src/vcfgenotypecompare.cpp.o -o vcfgenotypecompare -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 51%] Built target vcfgenotypecompare
make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfparsealts.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfparsealts.dir/build.make CMakeFiles/vcfparsealts.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 51%] Building CXX object CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -MF CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o.d -o CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp
[ 52%] Linking CXX executable vcfremoveaberrantgenotypes
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremoveaberrantgenotypes.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremoveaberrantgenotypes.dir/src/vcfremoveaberrantgenotypes.cpp.o -o vcfremoveaberrantgenotypes -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 52%] Built target vcfremoveaberrantgenotypes
make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstats.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfstats.dir/build.make CMakeFiles/vcfstats.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 52%] Building CXX object CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -MF CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o.d -o CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfstats.cpp
[ 52%] Linking CXX executable vcfsamplediff
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsamplediff.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsamplediff.dir/src/vcfsamplediff.cpp.o -o vcfsamplediff -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 52%] Built target vcfsamplediff
make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfflatten.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfflatten.dir/build.make CMakeFiles/vcfflatten.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 52%] Building CXX object CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -MF CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o.d -o CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfparsealts.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfstats.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfflatten.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 52%] Linking CXX executable vcfrandom
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandom.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandom.dir/src/vcfrandom.cpp.o -o vcfrandom -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 52%] Built target vcfrandom
make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfprimers.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfprimers.dir/build.make CMakeFiles/vcfprimers.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 53%] Building CXX object CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -MF CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o.d -o CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp
[ 54%] Linking CXX executable vcfparsealts
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfparsealts.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfparsealts.dir/src/vcfparsealts.cpp.o -o vcfparsealts -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 54%] Built target vcfparsealts
make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/depend
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfprimers.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfnumalt.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfnumalt.dir/build.make CMakeFiles/vcfnumalt.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 54%] Building CXX object CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -MF CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o.d -o CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfnumalt.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfnumalt.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 54%] Linking CXX executable vcfprimers
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfprimers.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfprimers.dir/src/vcfprimers.cpp.o -o vcfprimers -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 54%] Built target vcfprimers
make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcleancomplex.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfcleancomplex.dir/build.make CMakeFiles/vcfcleancomplex.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 55%] Building CXX object CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -MF CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o.d -o CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcleancomplex.cpp
[ 56%] Linking CXX executable vcfflatten
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfflatten.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfflatten.dir/src/vcfflatten.cpp.o -o vcfflatten -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 56%] Built target vcfflatten
make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfintersect.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfintersect.dir/build.make CMakeFiles/vcfintersect.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 56%] Building CXX object CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -MF CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o.d -o CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcleancomplex.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 57%] Linking CXX executable vcfnumalt
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfnumalt.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfnumalt.dir/src/vcfnumalt.cpp.o -o vcfnumalt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 57%] Built target vcfnumalt
make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfannotate.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfannotate.dir/build.make CMakeFiles/vcfannotate.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 58%] Building CXX object CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -MF CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o.d -o CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfintersect.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfannotate.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 59%] Linking CXX executable vcfstats
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstats.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstats.dir/src/vcfstats.cpp.o -o vcfstats -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 59%] Built target vcfstats
make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfallelicprimitives.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfallelicprimitives.dir/build.make CMakeFiles/vcfallelicprimitives.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 60%] Building CXX object CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -MF CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o.d -o CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp
[ 60%] Linking CXX executable vcfcleancomplex
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcleancomplex.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcleancomplex.dir/src/vcfcleancomplex.cpp.o -o vcfcleancomplex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 60%] Built target vcfcleancomplex
make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfoverlay.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfoverlay.dir/build.make CMakeFiles/vcfoverlay.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 60%] Building CXX object CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -MF CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o.d -o CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfoverlay.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:60,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:15:
/usr/include/c++/12/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const vcflib::VariantAllele&>, std::tuple<>}; _Key = vcflib::VariantAllele; _Val = std::pair<const vcflib::VariantAllele, double>; _KeyOfValue = std::_Select1st<std::pair<const vcflib::VariantAllele, double> >; _Compare = std::less<vcflib::VariantAllele>; _Alloc = std::allocator<std::pair<const vcflib::VariantAllele, double> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<vcflib::VariantAllele, std::pair<const vcflib::VariantAllele, double>, std::_Select1st<std::pair<const vcflib::VariantAllele, double> >, std::less<vcflib::VariantAllele>, std::allocator<std::pair<const vcflib::VariantAllele, double> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/map:61:
/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = vcflib::VariantAllele; _Tp = double; _Compare = std::less<vcflib::VariantAllele>; _Alloc = std::allocator<std::pair<const vcflib::VariantAllele, double> >]':
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<vcflib::VariantAllele, std::pair<const vcflib::VariantAllele, double>, std::_Select1st<std::pair<const vcflib::VariantAllele, double> >, std::less<vcflib::VariantAllele>, std::allocator<std::pair<const vcflib::VariantAllele, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<long unsigned int&&>, std::tuple<>}; _Key = long unsigned int; _Val = std::pair<const long unsigned int, vcflib::Variant>; _KeyOfValue = std::_Select1st<std::pair<const long unsigned int, vcflib::Variant> >; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, vcflib::Variant> >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<long unsigned int, std::pair<const long unsigned int, vcflib::Variant>, std::_Select1st<std::pair<const long unsigned int, vcflib::Variant> >, std::less<long unsigned int>, std::allocator<std::pair<const long unsigned int, vcflib::Variant> > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long unsigned int; _Tp = vcflib::Variant; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, vcflib::Variant> >]':
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<long unsigned int, std::pair<const long unsigned int, vcflib::Variant>, std::_Select1st<std::pair<const long unsigned int, vcflib::Variant> >, std::less<long unsigned int>, std::allocator<std::pair<const long unsigned int, vcflib::Variant> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[ 61%] Linking CXX executable vcfoverlay
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfoverlay.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfoverlay.dir/src/vcfoverlay.cpp.o -o vcfoverlay -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
[ 61%] Linking CXX executable vcfannotate
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfannotate.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfannotate.dir/src/vcfannotate.cpp.o -o vcfannotate -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 61%] Built target vcfoverlay
make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfaddinfo.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfaddinfo.dir/build.make CMakeFiles/vcfaddinfo.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 61%] Building CXX object CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -MF CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o.d -o CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 61%] Built target vcfannotate
make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepinfo.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfkeepinfo.dir/build.make CMakeFiles/vcfkeepinfo.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 62%] Building CXX object CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -MF CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o.d -o CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfaddinfo.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfkeepinfo.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = vcflib::VariantAllele; _Tp = double; _Compare = std::less<vcflib::VariantAllele>; _Alloc = std::allocator<std::pair<const vcflib::VariantAllele, double> >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:207:46:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<vcflib::VariantAllele, std::pair<const vcflib::VariantAllele, double>, std::_Select1st<std::pair<const vcflib::VariantAllele, double> >, std::less<vcflib::VariantAllele>, std::allocator<std::pair<const vcflib::VariantAllele, double> > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long unsigned int; _Tp = vcflib::Variant; _Compare = std::less<long unsigned int>; _Alloc = std::allocator<std::pair<const long unsigned int, vcflib::Variant> >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfallelicprimitives.cpp:306:46:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<long unsigned int, std::pair<const long unsigned int, vcflib::Variant>, std::_Select1st<std::pair<const long unsigned int, vcflib::Variant> >, std::less<long unsigned int>, std::allocator<std::pair<const long unsigned int, vcflib::Variant> > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
[ 63%] Linking CXX executable vcfintersect
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfintersect.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfintersect.dir/src/vcfintersect.cpp.o -o vcfintersect -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 63%] Built target vcfintersect
make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfkeepgeno.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfkeepgeno.dir/build.make CMakeFiles/vcfkeepgeno.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 64%] Building CXX object CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -MF CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o.d -o CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfkeepgeno.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 65%] Linking CXX executable vcfaddinfo
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfaddinfo.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfaddinfo.dir/src/vcfaddinfo.cpp.o -o vcfaddinfo -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 65%] Built target vcfaddinfo
make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfafpath.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfafpath.dir/build.make CMakeFiles/vcfafpath.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 65%] Building CXX object CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -MF CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o.d -o CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp
[ 65%] Linking CXX executable vcfkeepinfo
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepinfo.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepinfo.dir/src/vcfkeepinfo.cpp.o -o vcfkeepinfo -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 65%] Built target vcfkeepinfo
make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcountalleles.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfcountalleles.dir/build.make CMakeFiles/vcfcountalleles.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 65%] Building CXX object CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -MF CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o.d -o CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcountalleles.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcountalleles.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 65%] Linking CXX executable vcfallelicprimitives
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfallelicprimitives.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfallelicprimitives.dir/src/vcfallelicprimitives.cpp.o -o vcfallelicprimitives -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
[ 65%] Linking CXX executable vcfkeepgeno
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfkeepgeno.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfkeepgeno.dir/src/vcfkeepgeno.cpp.o -o vcfkeepgeno -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 65%] Built target vcfallelicprimitives
make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcflength.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcflength.dir/build.make CMakeFiles/vcflength.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 65%] Building CXX object CMakeFiles/vcflength.dir/src/vcflength.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcflength.dir/src/vcflength.cpp.o -MF CMakeFiles/vcflength.dir/src/vcflength.cpp.o.d -o CMakeFiles/vcflength.dir/src/vcflength.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcflength.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 65%] Built target vcfkeepgeno
make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfdistance.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfdistance.dir/build.make CMakeFiles/vcfdistance.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 65%] Building CXX object CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -MF CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o.d -o CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfafpath.cpp:78:26:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 66%] Linking CXX executable vcfcountalleles
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcountalleles.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcountalleles.dir/src/vcfcountalleles.cpp.o -o vcfcountalleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcflength.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 66%] Built target vcfcountalleles
make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfrandomsample.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfrandomsample.dir/build.make CMakeFiles/vcfrandomsample.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 67%] Building CXX object CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -MF CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o.d -o CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfdistance.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 68%] Linking CXX executable vcfafpath
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfafpath.dir/link.txt --verbose=1
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfrandomsample.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfafpath.dir/src/vcfafpath.cpp.o -o vcfafpath -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 68%] Built target vcfafpath
make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfentropy.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfentropy.dir/build.make CMakeFiles/vcfentropy.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 69%] Building CXX object CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -MF CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o.d -o CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfentropy.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfentropy.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 70%] Linking CXX executable vcflength
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcflength.dir/link.txt --verbose=1
[ 71%] Linking CXX executable vcfdistance
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfdistance.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcflength.dir/src/vcflength.cpp.o -o vcflength -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfdistance.dir/src/vcfdistance.cpp.o -o vcfdistance -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 71%] Built target vcflength
make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglxgt.dir/DependInfo.cmake --color=
[ 71%] Built target vcfdistance
make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfroc.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfglxgt.dir/build.make CMakeFiles/vcfglxgt.dir/build
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfroc.dir/build.make CMakeFiles/vcfroc.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 72%] Building CXX object CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -MF CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o.d -o CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp
[ 73%] Building CXX object CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -MF CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o.d -o CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfglxgt.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 74%] Linking CXX executable vcfrandomsample
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfrandomsample.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfrandomsample.dir/src/vcfrandomsample.cpp.o -o vcfrandomsample -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 74%] Built target vcfrandomsample
make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcheck.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfcheck.dir/build.make CMakeFiles/vcfcheck.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 74%] Building CXX object CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -MF CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o.d -o CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp
[ 74%] Linking CXX executable vcfentropy
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfentropy.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfentropy.dir/src/vcfentropy.cpp.o -o vcfentropy -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 74%] Built target vcfentropy
make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfstreamsort.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfstreamsort.dir/build.make CMakeFiles/vcfstreamsort.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 74%] Building CXX object CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -MF CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o.d -o CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcheck.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 74%] Linking CXX executable vcfglxgt
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglxgt.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglxgt.dir/src/vcfglxgt.cpp.o -o vcfglxgt -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 74%] Built target vcfglxgt
make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniq.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfuniq.dir/build.make CMakeFiles/vcfuniq.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 75%] Building CXX object CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -MF CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o.d -o CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfuniq.cpp
In file included from /usr/include/c++/12/map:60,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:15:
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<long double&&>, std::tuple<>}; _Key = long double; _Val = std::pair<const long double, std::vector<vcflib::Variant*> >; _KeyOfValue = std::_Select1st<std::pair<const long double, std::vector<vcflib::Variant*> > >; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::Variant*> > >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::Variant*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::Variant*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::Variant*> > > >::const_iterator' changed in GCC 7.1
2457 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 76%] Linking CXX executable vcfcheck
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcheck.dir/link.txt --verbose=1
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<long double&&>, std::tuple<>}; _Key = long double; _Val = std::pair<const long double, std::vector<vcflib::VariantAllele*> >; _KeyOfValue = std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcheck.dir/src/vcfcheck.cpp.o -o vcfcheck -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
/usr/include/c++/12/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const long double&>, std::tuple<>}; _Key = long double; _Val = std::pair<const long double, std::vector<vcflib::VariantAllele*> >; _KeyOfValue = std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]':
/usr/include/c++/12/bits/stl_tree.h:2457:7: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
[ 76%] Built target vcfcheck
make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfuniqalleles.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfuniqalleles.dir/build.make CMakeFiles/vcfuniqalleles.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 77%] Building CXX object CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -MF CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o.d -o CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp
In file included from /usr/include/c++/12/map:61:
/usr/include/c++/12/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector<vcflib::VariantAllele*>; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]':
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfuniq.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfuniqalleles.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 77%] Linking CXX executable vcfuniq
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniq.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniq.dir/src/vcfuniq.cpp.o -o vcfuniq -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 77%] Built target vcfuniq
make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfremap.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfremap.dir/build.make CMakeFiles/vcfremap.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 77%] Building CXX object CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -MF CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o.d -o CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfremap.cpp
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long double; _Tp = std::vector<vcflib::Variant*>; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::Variant*> > >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:257:33:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::Variant*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::Variant*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::Variant*> > > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long double; _Tp = std::vector<vcflib::VariantAllele*>; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:278:52:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector<vcflib::VariantAllele*>; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:305:50:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector<vcflib::VariantAllele*>; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:306:63:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector<vcflib::VariantAllele*>; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:314:50:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long double; _Tp = std::vector<vcflib::VariantAllele*>; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:316:63:
/usr/include/c++/12/bits/stl_map.h:511:44: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
511 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
512 | std::tuple<const key_type&>(__k),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
513 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long double; _Tp = std::vector<vcflib::VariantAllele*>; _Compare = std::less<long double>; _Alloc = std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfroc.cpp:384:88:
/usr/include/c++/12/bits/stl_map.h:530:44: note: parameter passing for argument of type 'std::_Rb_tree<long double, std::pair<const long double, std::vector<vcflib::VariantAllele*> >, std::_Select1st<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >, std::less<long double>, std::allocator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > > >::const_iterator' changed in GCC 7.1
530 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
531 | std::forward_as_tuple(std::move(__k)),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
532 | std::tuple<>());
| ~~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfremap.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
[ 77%] Linking CXX executable vcfuniqalleles
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfuniqalleles.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfuniqalleles.dir/src/vcfuniqalleles.cpp.o -o vcfuniqalleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 77%] Built target vcfuniqalleles
make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2fasta.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcf2fasta.dir/build.make CMakeFiles/vcf2fasta.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 78%] Building CXX object CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -MF CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o.d -o CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfstreamsort.cpp:117:71:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcf2fasta.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 78%] Linking CXX executable vcfroc
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfroc.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfroc.dir/src/vcfroc.cpp.o -o vcfroc -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 78%] Built target vcfroc
make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsitesummarize.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfsitesummarize.dir/build.make CMakeFiles/vcfsitesummarize.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 78%] Building CXX object CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -MF CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o.d -o CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp
[ 79%] Linking CXX executable vcfstreamsort
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfstreamsort.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfstreamsort.dir/src/vcfstreamsort.cpp.o -o vcfstreamsort -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 79%] Built target vcfstreamsort
make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfbreakmulti.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfbreakmulti.dir/build.make CMakeFiles/vcfbreakmulti.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 79%] Building CXX object CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -MF CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o.d -o CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsitesummarize.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 80%] Linking CXX executable vcfremap
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfremap.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfremap.dir/src/vcfremap.cpp.o -o vcfremap -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 80%] Built target vcfremap
make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcreatemulti.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfcreatemulti.dir/build.make CMakeFiles/vcfcreatemulti.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 80%] Building CXX object CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -MF CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o.d -o CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp
[ 81%] Linking CXX executable vcfsitesummarize
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsitesummarize.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsitesummarize.dir/src/vcfsitesummarize.cpp.o -o vcfsitesummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcreatemulti.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 81%] Built target vcfsitesummarize
make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfevenregions.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfevenregions.dir/build.make CMakeFiles/vcfevenregions.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 82%] Building CXX object CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -MF CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o.d -o CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
[ 82%] Linking CXX executable vcf2fasta
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2fasta.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2fasta.dir/src/vcf2fasta.cpp.o -o vcf2fasta -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 82%] Built target vcf2fasta
make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcat.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfcat.dir/build.make CMakeFiles/vcfcat.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 82%] Building CXX object CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -MF CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o.d -o CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcat.cpp
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfbreakmulti.cpp:100:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfevenregions.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcat.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 83%] Linking CXX executable vcfbreakmulti
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfbreakmulti.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfbreakmulti.dir/src/vcfbreakmulti.cpp.o -o vcfbreakmulti -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 83%] Built target vcfbreakmulti
make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosummarize.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfgenosummarize.dir/build.make CMakeFiles/vcfgenosummarize.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 84%] Building CXX object CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -MF CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o.d -o CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgenosummarize.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 84%] Linking CXX executable vcfevenregions
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfevenregions.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfevenregions.dir/src/vcfevenregions.cpp.o -o vcfevenregions -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
[ 85%] Linking CXX executable vcfcat
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcat.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcat.dir/src/vcfcat.cpp.o -o vcfcat -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 85%] Built target vcfevenregions
make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgenosamplenames.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfgenosamplenames.dir/build.make CMakeFiles/vcfgenosamplenames.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 86%] Building CXX object CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -MF CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o.d -o CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 86%] Built target vcfcat
make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2haplo.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfgeno2haplo.dir/build.make CMakeFiles/vcfgeno2haplo.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 87%] Building CXX object CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -MF CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o.d -o CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgeno2haplo.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgenosamplenames.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 88%] Linking CXX executable vcfcreatemulti
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcreatemulti.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcreatemulti.dir/src/vcfcreatemulti.cpp.o -o vcfcreatemulti -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 88%] Built target vcfcreatemulti
make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfleftalign.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfleftalign.dir/build.make CMakeFiles/vcfleftalign.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 88%] Building CXX object CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -MF CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o.d -o CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 89%] Linking CXX executable vcfgenosummarize
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosummarize.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosummarize.dir/src/vcfgenosummarize.cpp.o -o vcfgenosummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 89%] Built target vcfgenosummarize
make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfcombine.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfcombine.dir/build.make CMakeFiles/vcfcombine.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 90%] Building CXX object CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -MF CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o.d -o CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp
[ 90%] Linking CXX executable vcfgenosamplenames
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgenosamplenames.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgenosamplenames.dir/src/vcfgenosamplenames.cpp.o -o vcfgenosamplenames -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 90%] Built target vcfgenosamplenames
make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfgeno2alleles.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfgeno2alleles.dir/build.make CMakeFiles/vcfgeno2alleles.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 91%] Building CXX object CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -MF CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o.d -o CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfcombine.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfgeno2alleles.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator<double>]' at /usr/include/c++/12/bits/stl_vector.h:1294:21,
inlined from 'double entropy(const std::string&)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfleftalign.cpp:140:24:
/usr/include/c++/12/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
/usr/include/c++/12/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 91%] Linking CXX executable vcfgeno2alleles
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2alleles.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2alleles.dir/src/vcfgeno2alleles.cpp.o -o vcfgeno2alleles -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 91%] Built target vcfgeno2alleles
make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfindex.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfindex.dir/build.make CMakeFiles/vcfindex.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 92%] Building CXX object CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -MF CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o.d -o CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfindex.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfindex.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 93%] Linking CXX executable vcfleftalign
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfleftalign.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfleftalign.dir/src/vcfleftalign.cpp.o -o vcfleftalign -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 93%] Built target vcfleftalign
make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcf2dag.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcf2dag.dir/build.make CMakeFiles/vcf2dag.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 94%] Building CXX object CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -MF CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o.d -o CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp
[ 94%] Linking CXX executable vcfgeno2haplo
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfgeno2haplo.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfgeno2haplo.dir/src/vcfgeno2haplo.cpp.o -o vcfgeno2haplo -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 95%] Linking CXX executable vcfindex
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfindex.dir/link.txt --verbose=1
[ 95%] Built target vcfgeno2haplo
make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfsample2info.dir/DependInfo.cmake --color=
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfindex.dir/src/vcfindex.cpp.o -o vcfindex -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfsample2info.dir/build.make CMakeFiles/vcfsample2info.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 96%] Building CXX object CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -MF CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o.d -o CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcf2dag.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
[ 96%] Built target vcfindex
make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfqual2info.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfqual2info.dir/build.make CMakeFiles/vcfqual2info.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 97%] Building CXX object CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -MF CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o.d -o CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp
[ 97%] Linking CXX executable vcfcombine
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfcombine.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfcombine.dir/src/vcfcombine.cpp.o -o vcfcombine -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 97%] Built target vcfcombine
make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfo2qual.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfinfo2qual.dir/build.make CMakeFiles/vcfinfo2qual.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 97%] Building CXX object CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -MF CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o.d -o CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfqual2info.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/queue:62,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:23:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfinfo2qual.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfsample2info.cpp:194:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 97%] Linking CXX executable vcfqual2info
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfqual2info.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfqual2info.dir/src/vcfqual2info.cpp.o -o vcfqual2info -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 97%] Built target vcfqual2info
make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfglbound.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfglbound.dir/build.make CMakeFiles/vcfglbound.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 97%] Building CXX object CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -MF CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o.d -o CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp
[ 97%] Linking CXX executable vcfsample2info
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfsample2info.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfsample2info.dir/src/vcfsample2info.cpp.o -o vcfsample2info -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
[ 98%] Linking CXX executable vcfinfo2qual
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfo2qual.dir/link.txt --verbose=1
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfo2qual.dir/src/vcfinfo2qual.cpp.o -o vcfinfo2qual -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
[ 98%] Built target vcfsample2info
make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/depend
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
cd /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles/vcfinfosummarize.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make -f CMakeFiles/vcfinfosummarize.dir/build.make CMakeFiles/vcfinfosummarize.dir/build
make[4]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 98%] Building CXX object CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o
/usr/bin/c++ -DVCFLIB_VERSION=\"1.0.3\" -DVERSION=\"1.0.3\" -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/include -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/intervaltree -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/multichoose -I/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/filevercmp -isystem /usr/include/smithwaterman -isystem /usr/include/fastahack -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -MD -MT CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -MF CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o.d -o CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -c /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp
[ 98%] Linking CXX executable vcf2dag
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcf2dag.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcf2dag.dir/src/vcf2dag.cpp.o -o vcf2dag -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 98%] Built target vcfinfo2qual
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 98%] Built target vcf2dag
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp:10:
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/refwrap.h:39,
from /usr/include/c++/12/vector:66,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:13:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/queue:62,
from /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/Variant.h:23:
/usr/include/c++/12/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/12/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfglbound.cpp:137:34:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:70:
/usr/include/c++/12/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/12/bits/vector.tcc:439:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
439 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/vector:64:
In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]',
inlined from 'int main(int, char**)' at /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/src/vcfinfosummarize.cpp:204:31:
/usr/include/c++/12/bits/stl_vector.h:1287:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1287 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
[ 99%] Linking CXX executable vcfglbound
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfglbound.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfglbound.dir/src/vcfglbound.cpp.o -o vcfglbound -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[ 99%] Built target vcfglbound
[100%] Linking CXX executable vcfinfosummarize
/usr/bin/cmake -E cmake_link_script CMakeFiles/vcfinfosummarize.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++0x -D_FILE_OFFSET_BITS=64 -Isrc -O3 -fopenmp -Wl,-z,relro -Wl,-z,now -rdynamic CMakeFiles/vcfinfosummarize.dir/src/vcfinfosummarize.cpp.o -o vcfinfosummarize -Wl,-rpath,"\$ORIGIN:" libvcflib.so.1 -ltabixpp -DGIT_VERSION=0.9.0 -lhts -lz -llzma -lbz2 -lsmithwaterman -ldisorder -lfastahack -lssw -ltabixpp
make[4]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
[100%] Built target vcfinfosummarize
make[3]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -E cmake_progress_start /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/CMakeFiles 0
make[2]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
markdown README.md > README.html
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
export LD_LIBRARY_PATH=/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf/:$LD_LIBRARY_PATH && cd test && /usr/bin/make
make[2]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/test'
g++ -Wall -std=c++0x -I../src -I../googletest/googletest/include/ -I../fastahack -I../smithwaterman/ -I../multichoose/ -I../filevercmp/ -I../googletest/googletest/make/ tests/mainTest.cpp -o tests/main -lvcflib -lgtest_main -lgtest -L../obj-arm-linux-gnueabihf/ -L../googletest/googletest/make/ -lm -ltabixpp -lhts -lpthread
In file included from tests/variantTests.h:2,
from tests/mainTest.cpp:4:
../src/Variant.h:651:28: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
651 | struct stringcasecmp : binary_function<string, string, bool> {
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/12/bits/unique_ptr.h:37,
from /usr/include/c++/12/memory:76,
from /usr/include/gtest/gtest.h:54,
from tests/mainTest.cpp:3:
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
../src/Variant.h:652:42: warning: 'template<class _Arg1, class _Arg2, class _Result> struct std::binary_function' is deprecated [-Wdeprecated-declarations]
652 | struct charcasecmp : public std::binary_function<unsigned char, unsigned char, bool> {
| ^~~~~~~~~~~~~~~
/usr/include/c++/12/bits/stl_function.h:131:12: note: declared here
131 | struct binary_function
| ^~~~~~~~~~~~~~~
./tests/main
[==========] Running 5 tests from 2 test suites.
[----------] Global test environment set-up.
[----------] 1 test from Variant
[ RUN ] Variant.correctGenotype
[ OK ] Variant.correctGenotype (6630 ms)
[----------] 1 test from Variant (6630 ms total)
[----------] 4 tests from VariantCallFile
[ RUN ] VariantCallFile.open
[ OK ] VariantCallFile.open (0 ms)
[ RUN ] VariantCallFile.recordCountUncompressed
[ OK ] VariantCallFile.recordCountUncompressed (0 ms)
[ RUN ] VariantCallFile.recordCountCompressed
[ OK ] VariantCallFile.recordCountCompressed (8 ms)
[ RUN ] VariantCallFile.sampleNamesCompressed
[ OK ] VariantCallFile.sampleNamesCompressed (3 ms)
[----------] 4 tests from VariantCallFile (12 ms total)
[----------] Global test environment tear-down
[==========] 5 tests from 2 test suites ran. (6643 ms total)
[ PASSED ] 5 tests.
make[2]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/test'
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
create-stamp debian/debhelper-build-stamp
dh_testroot -a -O--buildsystem=cmake
dh_prep -a -O--buildsystem=cmake
dh_auto_install -a -O--buildsystem=cmake
cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/<<BUILDDIR>>/libvcflib-1.0.3\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true"
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
/usr/bin/cmake -S/<<BUILDDIR>>/libvcflib-1.0.3+dfsg -B/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0
make -f CMakeFiles/Makefile2 preinstall
make[2]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
make[2]: Nothing to be done for 'preinstall'.
make[2]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
Install the project...
/usr/bin/cmake -P cmake_install.cmake
-- Install configuration: "None"
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfecho
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfecho" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/dumpContigsFromHeader
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/dumpContigsFromHeader" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/bFst
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/bFst" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/pVst
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/pVst" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/hapLrt
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/hapLrt" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/popStats
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/popStats" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/wcFst
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/wcFst" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/iHS
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/iHS" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/segmentFst
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/segmentFst" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/segmentIhs
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/segmentIhs" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/genotypeSummary
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/genotypeSummary" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/sequenceDiversity
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/sequenceDiversity" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/pFst
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/pFst" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/smoother
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/smoother" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfld
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfld" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/plotHaps
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/plotHaps" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/abba-baba
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/abba-baba" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/permuteGPAT++
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/permuteGPAT++" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/permuteSmooth
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/permuteSmooth" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/normalize-iHS
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/normalize-iHS" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/meltEHH
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/meltEHH" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfaltcount
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfaltcount" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfhetcount
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfhetcount" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfhethomratio
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfhethomratio" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffilter
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffilter" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2tsv
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2tsv" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenotypes
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenotypes" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfannotategenotypes
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfannotategenotypes" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcommonsamples
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcommonsamples" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremovesamples
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremovesamples" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepsamples
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepsamples" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsamplenames
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsamplenames" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenotypecompare
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenotypecompare" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffixup
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffixup" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfclassify
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfclassify" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsamplediff
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsamplediff" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremoveaberrantgenotypes
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremoveaberrantgenotypes" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfrandom
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfrandom" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfparsealts
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfparsealts" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfstats
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfstats" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfflatten
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfflatten" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfprimers
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfprimers" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnumalt
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnumalt" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcleancomplex
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcleancomplex" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfintersect
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfintersect" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfannotate
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfannotate" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfallelicprimitives
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfallelicprimitives" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfoverlay
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfoverlay" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfaddinfo
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfaddinfo" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepinfo
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepinfo" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepgeno
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfkeepgeno" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfafpath
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfafpath" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcountalleles
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcountalleles" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcflength
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcflength" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfdistance
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfdistance" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfrandomsample
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfrandomsample" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfentropy
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfentropy" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfglxgt
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfglxgt" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfroc
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfroc" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcheck
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcheck" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfstreamsort
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfstreamsort" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfuniq
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfuniq" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfuniqalleles
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfuniqalleles" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremap
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremap" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2fasta
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2fasta" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsitesummarize
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsitesummarize" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfbreakmulti
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfbreakmulti" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcreatemulti
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcreatemulti" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfevenregions
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfevenregions" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcat
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcat" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenosummarize
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenosummarize" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenosamplenames
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgenosamplenames" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgeno2haplo
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgeno2haplo" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfleftalign
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfleftalign" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcombine
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcombine" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgeno2alleles
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgeno2alleles" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfindex
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfindex" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2dag
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2dag" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsample2info
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsample2info" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfqual2info
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfqual2info" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfinfo2qual
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfinfo2qual" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfglbound
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfglbound" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfinfosummarize
-- Set runtime path of "/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfinfosummarize" to ""
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/bed2region
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/bgziptabix
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2bed.py
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf2sqlite.py
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfbiallelic
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfclearid
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfclearinfo
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfcomplex
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcffirstheader
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfgtcompare.sh
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfindelproximity
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfindels
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfjoincalls
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfmultiallelic
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfmultiway
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfmultiwayscripts
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnobiallelicsnps
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnoindels
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnosnps
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfnulldotslashdot
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfplotaltdiscrepancy.r
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfplotaltdiscrepancy.sh
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfplotsitediscrepancy.r
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfplottstv.sh
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfprintaltdiscrepancy.r
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfprintaltdiscrepancy.sh
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfqualfilter
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfregionreduce
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfregionreduce_and_cut
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfregionreduce_pipe
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfregionreduce_uncompressed
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfremovenonATGC
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsnps
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfsort
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcf_strip_extra_headers
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/bin/vcfvarstats
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libvcflib.so.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/lib/arm-linux-gnueabihf/libvcflib.so
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/filevercmp.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/IntervalTree.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/catch.hpp
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/multichoose.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/multipermute.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/BedReader.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/Variant.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/cdflib.hpp
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/convert.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/gpatInfo.hpp
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/join.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/makeUnique.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/mt19937ar.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/pdflib.hpp
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/rnglib.hpp
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/split.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/var.hpp
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/vec128int.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/include/veclib_types.h
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfrandomsample.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfinfosummarize.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/sequenceDiversity.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepsamples.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/abba-baba.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfparsealts.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2fasta.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenosamplenames.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/iHS.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcreatemulti.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfuniqalleles.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/pFst.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2haplo.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcffilter.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremovesamples.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfclassify.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcombine.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfevenregions.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/segmentFst.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcflib.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/dumpContigsFromHeader.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/segmentIhs.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfnulldotslashdot.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/permuteSmooth.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfecho.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2tsv.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfglbound.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfld.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfentropy.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgeno2alleles.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenotypes.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfintersect.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfuniq.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/smoother.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfallelicprimitives.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsamplenames.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfindex.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfaddinfo.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfqual2info.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcat.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfglxgt.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfroc.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/popStats.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcheck.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/pVst.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremap.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfannotategenotypes.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstats.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcleancomplex.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfflatten.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/genotypeSummary.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfnumalt.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfoverlay.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfrandom.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfaltcount.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsamplediff.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfstreamsort.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/hapLrt.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/bFst.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfremoveaberrantgenotypes.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/plotHaps.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsitesummarize.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/permuteGPAT++.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcflength.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfbreakmulti.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenotypecompare.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/wcFst.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfannotate.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcffixup.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhetcount.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/normalize-iHS.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfdistance.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfinfo2qual.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcountalleles.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepgeno.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcf2dag.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfafpath.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfprimers.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/meltEHH.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfsample2info.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfleftalign.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfcommonsamples.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfkeepinfo.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfgenosummarize.1
-- Installing: /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/tmp/usr/man/man1/vcfhethomratio.1
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg/obj-arm-linux-gnueabihf'
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_install
find debian -name filevercmp.h -delete
cp -a filevercmp/filevercmp.h debian/libvcflib-dev/usr/include/vcflib/
mkdir -p debian/libvcflib-dev/usr/include/intervaltree
mv debian/libvcflib-dev/usr/include/vcflib/IntervalTree.h debian/libvcflib-dev/usr/include/intervaltree
# install pkg-config file
mkdir -p /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/libvcflib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
mv libvcflib.pc /<<BUILDDIR>>/libvcflib-1.0.3+dfsg/debian/libvcflib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
rm -rf debian/*/usr/lib/vcflib/bin/*.R
for pl in `grep -Rl '#!/usr/bin/env' debian/*/usr/*` ; do \
sed -i '1s?^#!/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' ${pl} ; \
done
grep: debian/libvcflib-dev/usr/lib/arm-linux-gnueabihf/libvcflib.so: No such file or directory
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_installdocs -a -O--buildsystem=cmake
dh_installchangelogs -a -O--buildsystem=cmake
dh_installman -a -O--buildsystem=cmake
dh_installsystemduser -a -O--buildsystem=cmake
dh_lintian -a -O--buildsystem=cmake
dh_perl -a -O--buildsystem=cmake
debian/rules override_dh_link
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_link
for rscript in debian/libvcflib-tools/usr/lib/vcflib/scripts/*.R ; do \
scriptname=$(basename $rscript) ; \
dh_link -p libvcflib-tools usr/lib/vcflib/scripts/$scriptname usr/lib/R/site-library/vcflib/$scriptname ; \
done
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_strip_nondeterminism -a -O--buildsystem=cmake
dh_compress -a -O--buildsystem=cmake
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_fixperms
chmod -x debian/*/usr/lib/vcflib/scripts/*.R
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.3+dfsg'
dh_missing -a -O--buildsystem=cmake
dh_dwz -a -O--buildsystem=cmake
dh_strip -a -O--buildsystem=cmake
dh_makeshlibs -a -O--buildsystem=cmake
dh_shlibdeps -a -O--buildsystem=cmake
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcat contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/permuteGPAT++ contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfbreakmulti contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcountalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/libvcflib1/usr/lib/arm-linux-gnueabihf/libvcflib.so.1 found in none of the libraries
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libvcflib1/usr/lib/arm-linux-gnueabihf/libvcflib.so.1 was not linked against libdisorder.so.0 (it uses none of the library's symbols)
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremap contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsample2info contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfprimers contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfleftalign contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcf2tsv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenosummarize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfhethomratio contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfhetcount contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepsamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfld contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/dumpContigsFromHeader contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfinfosummarize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfnumalt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/bFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcffilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfentropy contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/normalize-iHS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/hapLrt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfaltcount contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/wcFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2haplo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfdistance contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/meltEHH contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfuniqalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcffixup contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/segmentIhs contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfannotategenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcombine contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfflatten contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfintersect contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfclassify contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2fasta contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/permuteSmooth contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/plotHaps contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcffixup contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfkeepinfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/pVst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstreamsort contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/sequenceDiversity contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcleancomplex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfglxgt contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfecho contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremoveaberrantgenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/abba-baba contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenotypes contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfqual2info contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/iHS contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcreatemulti contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfglbound contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepinfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/genotypeSummary contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfparsealts contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/popStats contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/pFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfevenregions contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfallelicprimitives contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfrandom contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsitesummarize contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfoverlay contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniqalleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfindex contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfrandomsample contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcffilter contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2tsv contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2dag contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2alleles contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniq contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplenames contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/segmentFst contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfannotate contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcflength contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplediff contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfroc contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenosamplenames contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfaddinfo contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/bin/vcfallelicprimitives contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcommonsamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfinfo2qual contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenotypecompare contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfafpath contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepgeno contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/smoother contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremovesamples contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcheck contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dh_installdeb -a -O--buildsystem=cmake
dh_gencontrol -a -O--buildsystem=cmake
dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined
dpkg-gencontrol: warning: package libvcflib-tools: substitution variable ${perl:Depends} unused, but is defined
dh_md5sums -a -O--buildsystem=cmake
dh_builddeb -a -O--buildsystem=cmake
dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.3+dfsg-2_armhf.deb'.
dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.3+dfsg-2_armhf.deb'.
dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.3+dfsg-2_armhf.deb'.
dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.3+dfsg-2_armhf.deb'.
dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.3+dfsg-2_armhf.deb'.
dpkg-genbuildinfo --build=any -O../libvcflib_1.0.3+dfsg-2_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -O../libvcflib_1.0.3+dfsg-2_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2022-10-10T05:46:33Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
libvcflib_1.0.3+dfsg-2_armhf.changes:
-------------------------------------
Format: 1.8
Date: Fri, 07 Oct 2022 16:26:06 +0200
Source: libvcflib
Binary: libvcflib-dev libvcflib-tools libvcflib-tools-dbgsym libvcflib1 libvcflib1-dbgsym
Architecture: armhf
Version: 1.0.3+dfsg-2
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian mythic lxc autobuilder 1 <root@raspbian.org>
Changed-By: Andreas Tille <tille@debian.org>
Description:
libvcflib-dev - C++ library for parsing and manipulating VCF files (development)
libvcflib-tools - C++ library for parsing and manipulating VCF files (tools)
libvcflib1 - C++ library for parsing and manipulating VCF files
Changes:
libvcflib (1.0.3+dfsg-2) unstable; urgency=medium
.
* Fix watch file
* Standards-Version: 4.6.1 (routine-update)
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Files:
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20e9980bfc7fa3956f7bac76bf4fb261 16812760 debug optional libvcflib-tools-dbgsym_1.0.3+dfsg-2_armhf.deb
f63c02e880e39a3e86db0e5091213044 645316 science optional libvcflib-tools_1.0.3+dfsg-2_armhf.deb
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017339bcc0f905f097d2e9b09f1f41f8 7504 science optional libvcflib_1.0.3+dfsg-2_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libvcflib-dev_1.0.3+dfsg-2_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 85200 bytes: control archive=1668 bytes.
1268 bytes, 27 lines control
1548 bytes, 23 lines md5sums
Package: libvcflib-dev
Source: libvcflib
Version: 1.0.3+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 551
Depends: libvcflib1 (= 1.0.3+dfsg-2), libdisorder-dev, libfastahack-dev, libtabixpp-dev, libsmithwaterman-dev, libssw-dev
Section: libdevel
Priority: optional
Multi-Arch: same
Homepage: https://github.com/vcflib/vcflib
Description: C++ library for parsing and manipulating VCF files (development)
The Variant Call Format (VCF) is a flat-file, tab-delimited textual format
intended to concisely describe reference-indexed variations between
individuals. VCF provides a common interchange format for the description of
variation in individuals and populations of samples, and has become the defacto
standard reporting format for a wide array of genomic variant detectors.
.
vcflib provides methods to manipulate and interpret sequence variation as it
can be described by VCF. It is both:
.
* an API for parsing and operating on records of genomic variation as it can
be described by the VCF format,
* and a collection of command-line utilities for executing complex
manipulations on VCF files.
.
This package contains the static library and the header files.
drwxr-xr-x root/root 0 2022-10-07 14:26 ./
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/include/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/include/intervaltree/
-rw-r--r-- root/root 11829 2022-02-16 17:07 ./usr/include/intervaltree/IntervalTree.h
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/include/vcflib/
-rw-r--r-- root/root 5828 2022-02-16 17:06 ./usr/include/vcflib/BedReader.h
-rw-r--r-- root/root 22863 2022-10-07 14:26 ./usr/include/vcflib/Variant.h
-rw-r--r-- root/root 368608 2022-02-16 17:07 ./usr/include/vcflib/catch.hpp
-rw-r--r-- root/root 6628 2022-02-16 17:06 ./usr/include/vcflib/cdflib.hpp
-rw-r--r-- root/root 697 2022-02-16 17:06 ./usr/include/vcflib/convert.h
-rw-r--r-- root/root 1777 2022-02-16 17:07 ./usr/include/vcflib/filevercmp.h
-rw-r--r-- root/root 2053 2022-02-16 17:06 ./usr/include/vcflib/gpatInfo.hpp
-rw-r--r-- root/root 1238 2022-02-16 17:06 ./usr/include/vcflib/join.h
-rw-r--r-- root/root 194 2022-02-16 17:06 ./usr/include/vcflib/makeUnique.h
-rw-r--r-- root/root 6580 2022-02-16 17:06 ./usr/include/vcflib/mt19937ar.h
-rw-r--r-- root/root 2155 2022-02-16 17:07 ./usr/include/vcflib/multichoose.h
-rw-r--r-- root/root 3446 2022-02-16 17:07 ./usr/include/vcflib/multipermute.h
-rw-r--r-- root/root 2507 2022-02-16 17:06 ./usr/include/vcflib/pdflib.hpp
-rw-r--r-- root/root 1295 2022-02-16 17:06 ./usr/include/vcflib/rnglib.hpp
-rw-r--r-- root/root 1825 2022-02-16 17:06 ./usr/include/vcflib/split.h
-rw-r--r-- root/root 2311 2022-02-16 17:06 ./usr/include/vcflib/var.hpp
-rw-r--r-- root/root 75596 2022-02-16 17:06 ./usr/include/vcflib/vec128int.h
-rw-r--r-- root/root 14148 2022-02-16 17:06 ./usr/include/vcflib/veclib_types.h
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/lib/arm-linux-gnueabihf/libvcflib.so -> libvcflib.so.1
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 283 2022-10-07 14:26 ./usr/lib/arm-linux-gnueabihf/pkgconfig/libvcflib.pc
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/share/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/share/doc/libvcflib-dev/
-rw-r--r-- root/root 2253 2022-10-07 14:26 ./usr/share/doc/libvcflib-dev/changelog.Debian.gz
-rw-r--r-- root/root 2044 2022-10-07 14:26 ./usr/share/doc/libvcflib-dev/copyright
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/share/lintian/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 91 2022-10-07 14:26 ./usr/share/lintian/overrides/libvcflib-dev
libvcflib-tools-dbgsym_1.0.3+dfsg-2_armhf.deb
---------------------------------------------
new Debian package, version 2.0.
size 16812760 bytes: control archive=4288 bytes.
3770 bytes, 12 lines control
8893 bytes, 84 lines md5sums
Package: libvcflib-tools-dbgsym
Source: libvcflib
Version: 1.0.3+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 17756
Depends: libvcflib-tools (= 1.0.3+dfsg-2)
Section: debug
Priority: optional
Description: debug symbols for libvcflib-tools
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libvcflib-tools_1.0.3+dfsg-2_armhf.deb
--------------------------------------
new Debian package, version 2.0.
size 645316 bytes: control archive=6648 bytes.
1518 bytes, 29 lines control
17697 bytes, 258 lines md5sums
Package: libvcflib-tools
Source: libvcflib
Version: 1.0.3+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 6603
Depends: libc6 (>= 2.34), libdisorder0 (>= 0.0.2), libfastahack0 (>= 1.0.0+dfsg), libgcc-s1 (>= 3.5), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 11), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.3+dfsg), python3:any, r-base-core, r-cran-plyr, r-cran-ggplot2, r-cran-gridbase
Suggests: r-cran-pracma
Breaks: libvcflib1 (<= 1.0.0~rc2+dfsg-3)
Replaces: libvcflib1 (<= 1.0.0~rc2+dfsg-3)
Section: science
Priority: optional
Homepage: https://github.com/vcflib/vcflib
Description: C++ library for parsing and manipulating VCF files (tools)
The Variant Call Format (VCF) is a flat-file, tab-delimited textual format
intended to concisely describe reference-indexed variations between
individuals. VCF provides a common interchange format for the description of
variation in individuals and populations of samples, and has become the defacto
standard reporting format for a wide array of genomic variant detectors.
.
vcflib provides methods to manipulate and interpret sequence variation as it
can be described by VCF. It is both:
.
* an API for parsing and operating on records of genomic variation as it can
be described by the VCF format,
* and a collection of command-line utilities for executing complex
manipulations on VCF files.
.
This package contains several tools using the library.
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-rwxr-xr-x root/root 132816 2022-10-07 14:26 ./usr/bin/vcfallelicprimitives
-rwxr-xr-x root/root 67376 2022-10-07 14:26 ./usr/bin/vcffilter
-rwxr-xr-x root/root 67168 2022-10-07 14:26 ./usr/bin/vcffixup
-rwxr-xr-x root/root 67168 2022-10-07 14:26 ./usr/bin/vcfkeepinfo
-rwxr-xr-x root/root 404 2022-10-07 14:26 ./usr/bin/vcflib
lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/bin/vcfstreamsort -> ../lib/vcflib/bin/vcfstreamsort
lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/bin/vcfuniq -> ../lib/vcflib/bin/vcfuniq
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lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/lib/R/site-library/vcflib/plotBfst.R -> ../../../vcflib/scripts/plotBfst.R
lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/lib/R/site-library/vcflib/plotHapLrt.R -> ../../../vcflib/scripts/plotHapLrt.R
lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/lib/R/site-library/vcflib/plotHaplotypes.R -> ../../../vcflib/scripts/plotHaplotypes.R
lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/lib/R/site-library/vcflib/plotPfst.R -> ../../../vcflib/scripts/plotPfst.R
lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/lib/R/site-library/vcflib/plotSmoothed.R -> ../../../vcflib/scripts/plotSmoothed.R
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lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/lib/R/site-library/vcflib/plotXPEHH.R -> ../../../vcflib/scripts/plotXPEHH.R
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libvcflib1-dbgsym_1.0.3+dfsg-2_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 1441820 bytes: control archive=556 bytes.
409 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libvcflib1-dbgsym
Source: libvcflib
Version: 1.0.3+dfsg-2
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1496
Depends: libvcflib1 (= 1.0.3+dfsg-2)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libvcflib1
Build-Ids: 984618f86e0ca5dd46b5229c28bb28e9720887d1
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drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/lib/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/lib/debug/.build-id/
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lrwxrwxrwx root/root 0 2022-10-07 14:26 ./usr/share/doc/libvcflib1-dbgsym -> libvcflib1
libvcflib1_1.0.3+dfsg-2_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 126236 bytes: control archive=1216 bytes.
1251 bytes, 25 lines control
298 bytes, 4 lines md5sums
39 bytes, 1 lines shlibs
67 bytes, 2 lines triggers
Package: libvcflib1
Source: libvcflib
Version: 1.0.3+dfsg-2
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 341
Depends: libc6 (>= 2.29), libdisorder0 (>= 0.0.2), libfastahack0 (>= 1.0.0+dfsg), libgcc-s1 (>= 3.5), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 11), libtabixpp0 (>= 1.0.0)
Section: libs
Priority: optional
Multi-Arch: same
Homepage: https://github.com/vcflib/vcflib
Description: C++ library for parsing and manipulating VCF files
The Variant Call Format (VCF) is a flat-file, tab-delimited textual format
intended to concisely describe reference-indexed variations between
individuals. VCF provides a common interchange format for the description of
variation in individuals and populations of samples, and has become the defacto
standard reporting format for a wide array of genomic variant detectors.
.
vcflib provides methods to manipulate and interpret sequence variation as it
can be described by VCF. It is both:
.
* an API for parsing and operating on records of genomic variation as it can
be described by the VCF format,
* and a collection of command-line utilities for executing complex
manipulations on VCF files.
drwxr-xr-x root/root 0 2022-10-07 14:26 ./
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/lib/
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-rw-r--r-- root/root 329924 2022-10-07 14:26 ./usr/lib/arm-linux-gnueabihf/libvcflib.so.1
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drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/share/doc/
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-rw-r--r-- root/root 2044 2022-10-07 14:26 ./usr/share/doc/libvcflib1/copyright
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/share/lintian/
drwxr-xr-x root/root 0 2022-10-07 14:26 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 88 2022-10-07 14:26 ./usr/share/lintian/overrides/libvcflib1
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 404584
Build-Time: 398
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 218
Job: libvcflib_1.0.3+dfsg-2
Machine Architecture: armhf
Package: libvcflib
Package-Time: 637
Source-Version: 1.0.3+dfsg-2
Space: 404584
Status: successful
Version: 1.0.3+dfsg-2
--------------------------------------------------------------------------------
Finished at 2022-10-10T05:46:33Z
Build needed 00:10:37, 404584k disk space