libvcflib →
1.0.1+dfsg-3+b5 →
armhf → 2020-05-30 20:45:51
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-04
+==============================================================================+
| libvcflib 1.0.1+dfsg-3+b5 (armhf) Sat, 30 May 2020 20:17:25 +0000 |
+==============================================================================+
Package: libvcflib
Version: 1.0.1+dfsg-3+b5
Source Version: 1.0.1+dfsg-3
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-87c5fe08-a1f6-4038-bb3d-4693cbaa6d8a' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.7 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.5 MB in 25s (999 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| 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 7543 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main libvcflib 1.0.1+dfsg-3 (dsc) [2331 B]
Get:2 http://172.17.0.1/private bullseye-staging/main libvcflib 1.0.1+dfsg-3 (tar) [7528 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main libvcflib 1.0.1+dfsg-3 (diff) [12.6 kB]
Fetched 7543 kB in 1s (10.5 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/libvcflib-wO3Ww3/libvcflib-1.0.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/libvcflib-wO3Ww3' 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-eYvUBQ/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-eYvUBQ/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-eYvUBQ/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: 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 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: 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-eYvUBQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (2641 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:
libpam-cap netbase
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 32 not upgraded.
10 not fully installed or removed.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-eYvUBQ/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 (21.8 kB/s)
Setting up libudev1:armhf (245.5-3+rpi1) ...
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12233 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 libgcc1 (1:10.1.0-1+rpi1) ...
Setting up libgomp1:armhf (10.1.0-1+rpi1) ...
Setting up libatomic1:armhf (10.1.0-1+rpi1) ...
Setting up libfdisk1:armhf (2.35.1-5) ...
Setting up libubsan1:armhf (10.1.0-1+rpi1) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up libc-dev-bin (2.30-8+rpi1) ...
Setting up libcc1-0:armhf (10.1.0-1+rpi1) ...
Setting up fdisk (2.35.1-5) ...
Setting up libc6-dev:armhf (2.30-8+rpi1) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
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 (= 12), dh-exec, markdown, libtabixpp-dev, libbz2-dev, libdisorder-dev, libsmithwaterman-dev (>= 0.0+20160702-2), libssw-dev, libfastahack-dev (>= 0.0+git20160702.bbc645f+dfsg-5~), pkg-config, libipc-run3-perl
Filtered Build-Depends: debhelper-compat (= 12), dh-exec, markdown, libtabixpp-dev, libbz2-dev, libdisorder-dev, libsmithwaterman-dev (>= 0.0+20160702-2), libssw-dev, libfastahack-dev (>= 0.0+git20160702.bbc645f+dfsg-5~), pkg-config, libipc-run3-perl
dpkg-deb: building package 'sbuild-build-depends-libvcflib-dummy' in '/<<BUILDDIR>>/resolver-eYvUBQ/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-eYvUBQ/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ Sources [623 B]
Get:5 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ Packages [693 B]
Fetched 2649 B in 1s (3534 B/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:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libbz2-dev
libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libdisorder-dev
libdisorder0 libelf1 libfastahack-dev libfastahack0
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts3 libicu63 libipc-run3-perl libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libsmithwaterman-dev
libsmithwaterman0 libssh2-1 libssl1.1 libssw-dev libssw0
libsub-override-perl libtabixpp-dev libtabixpp0 libtinfo5 libtool
libuchardet0 libxml2 m4 man-db markdown pkg-config po-debconf sensible-utils
zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff krb5-doc
krb5-user 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 krb5-locales publicsuffix
libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-exec dh-strip-nondeterminism dwz file gettext gettext-base
groff-base intltool-debian libarchive-zip-perl libbrotli1 libbsd0 libbz2-dev
libcroco3 libcurl3-gnutls libdebhelper-perl libdeflate0 libdisorder-dev
libdisorder0 libelf1 libfastahack-dev libfastahack0
libfile-stripnondeterminism-perl libglib2.0-0 libgssapi-krb5-2 libhts-dev
libhts3 libicu63 libipc-run3-perl libk5crypto3 libkeyutils1 libkrb5-3
libkrb5support0 liblzma-dev libmagic-mgc libmagic1 libnghttp2-14
libpipeline1 libpsl5 librtmp1 libsigsegv2 libsmithwaterman-dev
libsmithwaterman0 libssh2-1 libssl1.1 libssw-dev libssw0
libsub-override-perl libtabixpp-dev libtabixpp0 libtinfo5 libtool
libuchardet0 libxml2 m4 man-db markdown pkg-config po-debconf
sbuild-build-depends-libvcflib-dummy sensible-utils zlib1g-dev
0 upgraded, 68 newly installed, 0 to remove and 32 not upgraded.
Need to get 27.4 MB of archives.
After this operation, 83.7 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-eYvUBQ/apt_archive ./ sbuild-build-depends-libvcflib-dummy 0.invalid.0 [976 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-1 [775 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.1 [187 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.8.1-1 [25.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.8.1-1 [14.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.2-1 [1158 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-5 [592 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.1 [1012 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf dh-exec armhf 0.23.2+b2 [25.7 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.7-6.1 [255 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libbz2-dev armhf 1.0.8-2 [27.7 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libkrb5support0 armhf 1.17-7+rpi1 [61.5 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libk5crypto3 armhf 1.17-7+rpi1 [112 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libkeyutils1 armhf 1.6.1-2 [14.5 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1g-1 [1272 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libkrb5-3 armhf 1.17-7+rpi1 [318 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libgssapi-krb5-2 armhf 1.17-7+rpi1 [135 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.40.0-1+b2 [74.2 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1 [53.9 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b1 [54.3 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.8.0-2.1 [126 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libcurl3-gnutls armhf 7.68.0-1 [284 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libdeflate0 armhf 1.6-1 [47.4 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libdisorder0 armhf 0.0.2+git20130809.8062ee1-1 [4568 B]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libdisorder-dev armhf 0.0.2+git20130809.8062ee1-1 [4156 B]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libfastahack0 armhf 1.0.0+dfsg-5 [20.1 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libfastahack-dev armhf 1.0.0+dfsg-5 [23.6 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libhts3 armhf 1.10.2-3 [319 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf liblzma-dev armhf 5.2.4-1 [203 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libhts-dev armhf 1.10.2-3 [4796 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libipc-run3-perl all 0.048-2 [34.2 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libsmithwaterman0 armhf 0.0+git20160702.2610e25-8 [31.1 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libsmithwaterman-dev armhf 0.0+git20160702.2610e25-8 [35.3 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libssw0 armhf 1.1-9 [21.5 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libssw-dev armhf 1.1-9 [24.8 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libtabixpp0 armhf 1.1.0-3 [8204 B]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libtabixpp-dev armhf 1.1.0-3 [7752 B]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf markdown all 1.0.1-10 [17.4 kB]
Get:68 http://172.17.0.1/private bullseye-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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No schema files found: doing nothing.
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Setting up libicu63:armhf (63.2-3) ...
Setting up libkrb5support0:armhf (1.17-7+rpi1) ...
Setting up libfastahack-dev (1.0.0+dfsg-5) ...
Setting up autotools-dev (20180224.1) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up pkg-config (0.29.2-1) ...
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Setting up libdisorder-dev:armhf (0.0.2+git20130809.8062ee1-1) ...
Setting up liblzma-dev:armhf (5.2.4-1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libipc-run3-perl (0.048-2) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libssh2-1:armhf (1.8.0-2.1) ...
Setting up libkrb5-3:armhf (1.17-7+rpi1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
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Setting up libxml2:armhf (2.9.10+dfsg-5) ...
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Setting up libbz2-dev:armhf (1.0.8-2) ...
Setting up libfile-stripnondeterminism-perl (1.8.1-1) ...
Setting up libssw-dev:armhf (1.1-9) ...
Setting up libtool (2.4.6-14) ...
Setting up m4 (1.4.18-4) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libgssapi-krb5-2:armhf (1.17-7+rpi1) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up libsmithwaterman-dev (0.0+git20160702.2610e25-8) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.8.1-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up automake (1:1.16.2-1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up libcurl3-gnutls:armhf (7.68.0-1) ...
Setting up man-db (2.9.1-1) ...
Not building database; man-db/auto-update is not 'true'.
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libhts3:armhf (1.10.2-3) ...
Setting up po-debconf (1.0.21) ...
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Setting up libtabixpp0:armhf (1.1.0-3) ...
Setting up libtabixpp-dev:armhf (1.1.0-3) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.1) ...
Setting up dh-exec (0.23.2+b2) ...
Setting up sbuild-build-depends-libvcflib-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.30-8+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.4-armmp armhf (armv7l)
Toolchain package versions: binutils_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-11+rpi1 gcc-9_9.3.0-11+rpi1 libc6-dev_2.30-8+rpi1 libstdc++-9-dev_9.3.0-11+rpi1 libstdc++6_10.1.0-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.1.0 autoconf_2.69-11.1 automake_1:1.16.2-1 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-6 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.35.1-5 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-11+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.1 debianutils_4.9.1 dh-autoreconf_19 dh-exec_0.23.2+b2 dh-strip-nondeterminism_1.8.1-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.24-1 fdisk_2.35.1-5 file_1:5.38-5 findutils_4.7.0-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.3.0-11+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10.1.0-1+rpi1 gcc-9_9.3.0-11+rpi1 gcc-9-base_9.3.0-11+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-3 libacl1_2.2.53-8 libapt-pkg6.0_2.1.0 libarchive-zip-perl_1.68-1 libasan5_9.3.0-11+rpi1 libassuan0_2.5.3-7 libatomic1_10.1.0-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3 libaudit1_1:2.8.5-3 libbinutils_2.34-5+rpi1 libblkid1_2.35.1-5 libbrotli1_1.0.7-6.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libbz2-dev_1.0.8-2 libc-bin_2.30-8+rpi1 libc-dev-bin_2.30-8+rpi1 libc6_2.30-8+rpi1 libc6-dev_2.30-8+rpi1 libcap-ng0_0.7.9-2.1+b1 libcap2_1:2.33-1 libcap2-bin_1:2.33-1 libcc1-0_10.1.0-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.16-1 libcrypt1_1:4.4.16-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libcurl3-gnutls_7.68.0-1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_13.1 libdeflate0_1.6-1 libdisorder-dev_0.0.2+git20130809.8062ee1-1 libdisorder0_0.0.2+git20130809.8062ee1-1 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfastahack-dev_1.0.0+dfsg-5 libfastahack0_1.0.0+dfsg-5 libfdisk1_2.35.1-5 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.8.1-1 libgcc-9-dev_9.3.0-11+rpi1 libgcc-s1_10.1.0-1+rpi1 libgcc1_1:10.1.0-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.64.2-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.13-2 libgomp1_10.1.0-1+rpi1 libgpg-error0_1.37-1 libgssapi-krb5-2_1.17-7+rpi1 libhogweed5_3.5.1+really3.5.1-2 libhts-dev_1.10.2-3 libhts3_1.10.2-3 libicu63_63.2-3 libidn2-0_2.3.0-1 libipc-run3-perl_0.048-2 libisl22_0.22.1-1 libk5crypto3_1.17-7+rpi1 libkeyutils1_1.6.1-2 libkrb5-3_1.17-7+rpi1 libkrb5support0_1.17-7+rpi1 libksba8_1.3.5-2 libldap-2.4-2_2.4.50+dfsg-1 libldap-common_2.4.50+dfsg-1 liblz4-1_1.9.2-2 liblzma-dev_5.2.4-1 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.35.1-5 libmpc3_1.1.0-1 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnghttp2-14_1.40.0-1+b2 libnpth0_1.6-1 libp11-kit0_0.23.20-1 libpam-cap_1:2.33-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-10 libpipeline1_1.5.2-2 libpsl5_0.21.0-1 libreadline7_7.0-5 libreadline8_8.0-4 librtmp1_2.4+20151223.gitfa8646d.1-2+b1 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1+b1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.35.1-5 libsmithwaterman-dev_0.0+git20160702.2610e25-8 libsmithwaterman0_0.0+git20160702.2610e25-8 libsqlite3-0_3.31.1-5 libss2_1.45.6-1 libssh2-1_1.8.0-2.1 libssl1.1_1.1.1g-1 libssw-dev_1.1-9 libssw0_1.1-9 libstdc++-9-dev_9.3.0-11+rpi1 libstdc++6_10.1.0-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_245.5-3+rpi1 libtabixpp-dev_1.1.0-3 libtabixpp0_1.1.0-3 libtasn1-6_4.16.0-2 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10.1.0-1+rpi1 libuchardet0_0.0.6-3 libudev1_245.5-3+rpi1 libunistring2_0.9.10-2 libuuid1_2.35.1-5 libxml2_2.9.10+dfsg-5 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-2 man-db_2.9.1-1 markdown_1.0.1-10 mawk_1.3.4.20200120-2 mount_2.35.1-2 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-10 perl-base_5.30.0-10 perl-modules-5.30_5.30.0-10 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-libvcflib-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 tzdata_2020a-1 util-linux_2.35.1-5 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Wed Feb 12 12:00:46 2020 UTC
gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./libvcflib_1.0.1+dfsg-3.dsc
dpkg-source: info: extracting libvcflib in /<<BUILDDIR>>/libvcflib-1.0.1+dfsg
dpkg-source: info: unpacking libvcflib_1.0.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking libvcflib_1.0.1+dfsg-3.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_tabixpp.patch
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 fix_ssw_cpp_header_name.patch
dpkg-source: info: applying dont_link_pthread
dpkg-source: info: applying override_version
dpkg-source: info: applying hardening-flags
dpkg-source: info: applying no_libVCFH
dpkg-source: info: applying disorder_include
dpkg-source: info: applying crossbuild
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 1.0.1+dfsg-3+b5
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=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-87c5fe08-a1f6-4038-bb3d-4693cbaa6d8a
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package libvcflib
dpkg-buildpackage: info: source version 1.0.1+dfsg-3+b5
dpkg-buildpackage: info: source distribution bullseye-staging
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean
dh_auto_clean
make -j4 clean
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
rm -f bin/vcfecho bin/vcfnormalizesvs bin/dumpContigsFromHeader bin/bFst bin/pVst bin/hapLrt bin/popStats bin/wcFst bin/iHS bin/segmentFst bin/segmentIhs bin/genotypeSummary bin/sequenceDiversity bin/pFst bin/smoother bin/vcfld bin/plotHaps bin/abba-baba bin/permuteGPAT++ bin/permuteSmooth bin/normalize-iHS bin/meltEHH bin/vcfaltcount bin/vcfhetcount bin/vcfhethomratio bin/vcffilter bin/vcf2tsv bin/vcfgenotypes bin/vcfannotategenotypes bin/vcfcommonsamples bin/vcfremovesamples bin/vcfkeepsamples bin/vcfsamplenames bin/vcfgenotypecompare bin/vcffixup bin/vcfclassify bin/vcfsamplediff bin/vcfremoveaberrantgenotypes bin/vcfrandom bin/vcfparsealts bin/vcfstats bin/vcfflatten bin/vcfprimers bin/vcfnumalt bin/vcfcleancomplex bin/vcfintersect bin/vcfannotate bin/vcfallelicprimitives bin/vcfoverlay bin/vcfaddinfo bin/vcfkeepinfo bin/vcfkeepgeno bin/vcfafpath bin/vcfcountalleles bin/vcflength bin/vcfdistance bin/vcfrandomsample bin/vcfentropy bin/vcfglxgt bin/vcfroc bin/vcfcheck bin/vcfstreamsort bin/vcfuniq bin/vcfuniqalleles bin/vcfremap bin/vcf2fasta bin/vcfsitesummarize bin/vcfbreakmulti bin/vcfcreatemulti bin/vcfevenregions bin/vcfcat bin/vcfgenosummarize bin/vcfgenosamplenames bin/vcfgeno2haplo bin/vcfleftalign bin/vcfcombine bin/vcfgeno2alleles bin/vcfindex bin/vcf2dag bin/vcfsample2info bin/vcfqual2info bin/vcfinfo2qual bin/vcfglbound bin/vcfunphase bin/vcfnull2ref bin/vcfinfosummarize src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o
rm -f libvcflib.so*
rm -f -r bin
rm -f -r lib
rm -f -r include
rm -f -r obj
make clean -C multichoose
make[2]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/multichoose'
rm -f cmultichoose
rm -f multichoose
rm -f multipermute
make[2]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/multichoose'
make clean -C test
make[2]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/test'
rm -f tests/main
make[2]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/test'
make clean -C filevercmp
make[2]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/filevercmp'
rm -f filevercmp
rm -f filevercmp.o
make[2]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/filevercmp'
make clean -C intervaltree
make[2]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/intervaltree'
rm -rf interval_tree_test stage
make[2]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/intervaltree'
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
debian/rules override_dh_clean
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
dh_clean
find . -name "*.o" -delete
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
debian/rules build-arch
dh build-arch
dh_update_autotools_config -a
dh_autoreconf -a
dh_auto_configure -a
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
dh_auto_build
make -j4 "INSTALL=install --strip-program=true"
make[2]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
if [ ! -d bin ]; then mkdir -p bin; fi
if [ ! -d lib ]; then mkdir -p lib; fi
if [ ! -d include ]; then mkdir -p include; fi
if [ ! -d obj ]; then mkdir -p obj; fi
cd multichoose && LDFLAGS="-Wl,-z,relro -Wl,-z,now" make && cp -f *.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
cd filevercmp && LDFLAGS="-Wl,-z,relro -Wl,-z,now" make && cp -f *.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/ && cp -f *.o /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
cd intervaltree && LDFLAGS="-Wl,-z,relro -Wl,-z,now" make && cp -f *.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
make[3]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/filevercmp'
make[3]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/multichoose'
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now multichoose.cpp -o multichoose
cc -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c filevercmp.c
make[3]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/intervaltree'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -Wall -Wl,-z,relro -Wl,-z,now interval_tree_test.cpp -std=c++0x -o interval_tree_test
g++ -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now multipermute.cpp -o multipermute
cc -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o filevercmp main.c filevercmp.o
make[3]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/filevercmp'
make[3]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/multichoose'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/Variant.o src/Variant.cpp -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm && cp -f src/*.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/rnglib.o src/rnglib.cpp -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm && cp -f src/*.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/var.o src/var.cpp -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm && cp -f src/*.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/pdflib.o src/pdflib.cpp -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm && cp -f src/*.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
In file included from /usr/include/c++/9/vector:72,
from src/var.hpp:8,
from src/var.cpp:2:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc: In member function 'virtual void genotype::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/var.hpp:8,
from src/var.cpp:2:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/var.hpp:8,
from src/var.cpp:2:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/var.hpp:8,
from src/var.cpp:2:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void pooled::loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, std::string, long int)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/var.hpp:8,
from src/var.cpp:2:
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/cdflib.o src/cdflib.cpp -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm && cp -f src/*.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
g++ -Wdate-time -D_FORTIFY_SOURCE=2 -c -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -fPIC -o src/split.o src/split.cpp -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm && cp -f src/*.h* /<<BUILDDIR>>/libvcflib-1.0.1+dfsg/include/
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from interval_tree_test.cpp:4:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Catch::SectionEndInfo&}; _Tp = Catch::SectionEndInfo; _Alloc = std::allocator<Catch::SectionEndInfo>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Catch::SectionEndInfo>::iterator' {aka '__gnu_cxx::__normal_iterator<Catch::SectionEndInfo*, std::vector<Catch::SectionEndInfo> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from interval_tree_test.cpp:4:
/usr/include/c++/9/bits/stl_vector.h: In member function 'virtual void Catch::RunContext::sectionEndedEarly(const Catch::SectionEndInfo&)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Catch::SectionEndInfo*, std::vector<Catch::SectionEndInfo> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In destructor 'Catch::Section::~Section()':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Catch::SectionEndInfo*, std::vector<Catch::SectionEndInfo> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from interval_tree_test.cpp:4:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Interval<unsigned int, double>&}; _Tp = Interval<unsigned int, double>; _Alloc = std::allocator<Interval<unsigned int, double> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > >::iterator' {aka '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void IntervalTree<Scalar, Value>::visit_near(const Scalar&, const Scalar&, UnaryFunction) const [with UnaryFunction = IntervalTree<Scalar, Value>::visit_overlapping(const Scalar&, const Scalar&, UnaryFunction) const [with UnaryFunction = IntervalTree<Scalar, Value>::findOverlapping(const Scalar&, const Scalar&) const [with Scalar = unsigned int; Value = double]::<lambda(const interval&)>; Scalar = unsigned int; Value = double]::<lambda(const interval&)>; Scalar = unsigned int; Value = double]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'IntervalTree<Scalar, Value>::interval_vector IntervalTree<Scalar, Value>::findOverlapping(const Scalar&, const Scalar&) const [with Scalar = unsigned int; Value = double]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Interval<double, unsigned int>&}; _Tp = Interval<double, unsigned int>; _Alloc = std::allocator<Interval<double, unsigned int> >]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > >::iterator' {aka '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void IntervalTree<Scalar, Value>::visit_near(const Scalar&, const Scalar&, UnaryFunction) const [with UnaryFunction = IntervalTree<Scalar, Value>::visit_overlapping(const Scalar&, const Scalar&, UnaryFunction) const [with UnaryFunction = IntervalTree<Scalar, Value>::findOverlapping(const Scalar&, const Scalar&) const [with Scalar = double; Value = unsigned int]::<lambda(const interval&)>; Scalar = double; Value = unsigned int]::<lambda(const interval&)>; Scalar = double; Value = unsigned int]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'IntervalTree<Scalar, Value>::interval_vector IntervalTree<Scalar, Value>::findOverlapping(const Scalar&, const Scalar&) const [with Scalar = double; Value = unsigned int]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
cc -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname -Wl,libvcflib.so.1 -o libvcflib.so.1 src/Variant.o src/rnglib.o src/var.o src/pdflib.o src/cdflib.o src/split.o filevercmp/filevercmp.o -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
ln -s libvcflib.so.1 libvcflib.so
cp -f -a libvcflib.so* lib
In file included from /usr/include/c++/9/algorithm:62,
from IntervalTree.h:5,
from interval_tree_test.cpp:7:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<IntervalTree<unsigned int, double>::IntervalStartCmp>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<IntervalTree<unsigned int, double>::IntervalStartCmp>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1820 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<IntervalTree<double, unsigned int>::IntervalStartCmp>]':
/usr/include/c++/9/bits/stl_algo.h:1820:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<IntervalTree<double, unsigned int>::IntervalStartCmp>]':
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from IntervalTree.h:5,
from interval_tree_test.cpp:7:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >; _Distance = int; _Tp = Interval<unsigned int, double>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<IntervalTree<unsigned int, double>::IntervalStartCmp>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from IntervalTree.h:5,
from interval_tree_test.cpp:7:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<IntervalTree<unsigned int, double>::IntervalStartCmp>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In constructor 'IntervalTree<Scalar, Value>::IntervalTree(IntervalTree<Scalar, Value>::interval_vector&&, std::size_t, std::size_t, std::size_t, Scalar, Scalar) [with Scalar = unsigned int; Value = double]':
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from interval_tree_test.cpp:4:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from IntervalTree.h:5,
from interval_tree_test.cpp:7:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<unsigned int, double>*, std::vector<Interval<unsigned int, double>, std::allocator<Interval<unsigned int, double> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algo.h:61,
from /usr/include/c++/9/algorithm:62,
from IntervalTree.h:5,
from interval_tree_test.cpp:7:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >; _Distance = int; _Tp = Interval<double, unsigned int>; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<IntervalTree<double, unsigned int>::IntervalStartCmp>]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from IntervalTree.h:5,
from interval_tree_test.cpp:7:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<IntervalTree<double, unsigned int>::IntervalStartCmp>]':
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1939 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1939:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1953:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1953 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h: In constructor 'IntervalTree<Scalar, Value>::IntervalTree(IntervalTree<Scalar, Value>::interval_vector&&, std::size_t, std::size_t, std::size_t, Scalar, Scalar) [with Scalar = double; Value = unsigned int]':
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1884:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1884 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1889:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1889 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from /usr/include/c++/9/bits/random.h:34,
from /usr/include/c++/9/random:49,
from interval_tree_test.cpp:4:
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from IntervalTree.h:5,
from interval_tree_test.cpp:7:
/usr/include/c++/9/bits/stl_algo.h:1967:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Interval<double, unsigned int>*, std::vector<Interval<double, unsigned int>, std::allocator<Interval<double, unsigned int> > > >' changed in GCC 7.1
1967 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1968 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1969 | __comp);
| ~~~~~~~
make[3]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/intervaltree'
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfecho.cpp -o bin/vcfecho -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfnormalizesvs.cpp -o bin/vcfnormalizesvs -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/dumpContigsFromHeader.cpp -o bin/dumpContigsFromHeader -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/bFst.cpp -o bin/bFst -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/pVst.cpp -o bin/pVst -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/hapLrt.cpp -o bin/hapLrt -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/popStats.cpp -o bin/popStats -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/bFst.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/bFst.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'void phardy(std::vector<double>&, double, double)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/bFst.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'void loadPop(std::vector<std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > > >&, pop&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/pVst.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/pVst.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'void calc(copyNcounts*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/pVst.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function '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> > > >&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/hapLrt.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/wcFst.cpp -o bin/wcFst -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/hapLrt.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/iHS.cpp -o bin/iHS -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/segmentFst.cpp -o bin/segmentFst -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/segmentIhs.cpp -o bin/segmentIhs -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/split.h:6,
from src/segmentFst.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/split.h:6,
from src/segmentIhs.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'int main(int, char**)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/genotypeSummary.cpp -o bin/genotypeSummary -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/map:60,
from src/Variant.h:6,
from src/iHS.cpp:1:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/Variant.h:6,
from src/iHS.cpp:1:
/usr/include/c++/9/bits/stl_map.h: In function 'void loadGeneticMap(int, int)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In function 'bool gDist(int, int, double*)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/sequenceDiversity.cpp -o bin/sequenceDiversity -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/iHS.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/pFst.cpp -o bin/pFst -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/iHS.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/smoother.cpp -o bin/smoother -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/sequenceDiversity.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/sequenceDiversity.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from src/smoother.cpp:4:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&>, std::tuple<>}; _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> > >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> > >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> > >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/smoother.cpp:4:
/usr/include/c++/9/bits/stl_map.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, std::fpos<__mbstate_t> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfld.cpp -o bin/vcfld -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/plotHaps.cpp -o bin/plotHaps -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/abba-baba.cpp -o bin/abba-baba -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/permuteGPAT++.cpp -o bin/permuteGPAT++ -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
src/abba-baba.cpp: In function 'int sample_het(int&)':
src/abba-baba.cpp:74:1: warning: no return statement in function returning non-void [-Wreturn-type]
74 | }
| ^
In file included from /usr/include/c++/9/vector:72,
from src/split.h:6,
from src/permuteGPAT++.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/split.h:6,
from src/permuteGPAT++.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfld.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/permuteSmooth.cpp -o bin/permuteSmooth -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/plotHaps.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/split.h:6,
from src/permuteSmooth.cpp:39:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/split.h:6,
from src/permuteSmooth.cpp:39:
/usr/include/c++/9/bits/stl_vector.h: In function 'bool getContiguousWindow(std::vector<score*>&, std::vector<double>&, int, int*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfld.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In function 'bool permute(double, int, std::vector<score*>&, double*, double*, double*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/plotHaps.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/normalize-iHS.cpp -o bin/normalize-iHS -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/meltEHH.cpp -o bin/meltEHH -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfaltcount.cpp -o bin/vcfaltcount -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/split.h:6,
from src/normalize-iHS.cpp:50:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/split.h:6,
from src/normalize-iHS.cpp:50:
/usr/include/c++/9/bits/stl_vector.h: In function 'void normalize(std::vector<iHSdat*>&, int*)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfhetcount.cpp -o bin/vcfhetcount -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfhethomratio.cpp -o bin/vcfhethomratio -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/map:60,
from src/Variant.h:6,
from src/meltEHH.cpp:1:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/Variant.h:6,
from src/meltEHH.cpp:1:
/usr/include/c++/9/bits/stl_map.h: In function 'void loadGeneticMap(int, int)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h: In function 'bool gDist(int, int, double*)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<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' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/meltEHH.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcffilter.cpp -o bin/vcffilter -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcf2tsv.cpp -o bin/vcf2tsv -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/meltEHH.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfgenotypes.cpp -o bin/vcfgenotypes -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfannotategenotypes.cpp -o bin/vcfannotategenotypes -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfcommonsamples.cpp -o bin/vcfcommonsamples -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfremovesamples.cpp -o bin/vcfremovesamples -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfkeepsamples.cpp -o bin/vcfkeepsamples -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfsamplenames.cpp -o bin/vcfsamplenames -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfgenotypecompare.cpp -o bin/vcfgenotypecompare -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/map:60,
from src/Variant.h:6,
from src/vcfannotategenotypes.cpp:1:
/usr/include/c++/9/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >'} changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcffixup.cpp -o bin/vcffixup -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfclassify.cpp -o bin/vcfclassify -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfannotategenotypes.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' {aka '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfannotategenotypes.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/Variant.h:6,
from src/vcfannotategenotypes.cpp:1:
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> >, vcflib::Variant> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfsamplediff.cpp -o bin/vcfsamplediff -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfremoveaberrantgenotypes.cpp -o bin/vcfremoveaberrantgenotypes -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfrandom.cpp -o bin/vcfrandom -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfparsealts.cpp -o bin/vcfparsealts -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfstats.cpp -o bin/vcfstats -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfflatten.cpp -o bin/vcfflatten -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfprimers.cpp -o bin/vcfprimers -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfnumalt.cpp -o bin/vcfnumalt -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfcleancomplex.cpp -o bin/vcfcleancomplex -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfintersect.cpp -o bin/vcfintersect -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfannotate.cpp -o bin/vcfannotate -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfallelicprimitives.cpp -o bin/vcfallelicprimitives -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfoverlay.cpp -o bin/vcfoverlay -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/map:60,
from src/Variant.h:6,
from src/vcfoverlay.cpp:1:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> >; _KeyOfValue = std::_Select1st<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > >]':
/usr/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> >, std::_Select1st<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:60,
from src/Variant.h:6,
from src/vcfallelicprimitives.cpp:1:
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long unsigned int, vcflib::Variant> >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/map:61,
from src/Variant.h:6,
from src/vcfoverlay.cpp:1:
/usr/include/c++/9/bits/stl_map.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> >, std::_Select1st<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<int, std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> >, std::_Select1st<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > >, std::less<int>, std::allocator<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > > >::const_iterator' {aka 'std::_Rb_tree_const_iterator<std::pair<const int, std::pair<vcflib::VariantCallFile*, vcflib::Variant> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfaddinfo.cpp -o bin/vcfaddinfo -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
/usr/include/c++/9/bits/stl_tree.h: In member function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple<const 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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const vcflib::VariantAllele, double> >'} changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfkeepinfo.cpp -o bin/vcfkeepinfo -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/map:61,
from src/Variant.h:6,
from src/vcfallelicprimitives.cpp:1:
/usr/include/c++/9/bits/stl_map.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const vcflib::VariantAllele, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long unsigned int, vcflib::Variant> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long unsigned int, vcflib::Variant> >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<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' {aka 'std::_Rb_tree_const_iterator<std::pair<const vcflib::VariantAllele, double> >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfkeepgeno.cpp -o bin/vcfkeepgeno -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfafpath.cpp -o bin/vcfafpath -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfcountalleles.cpp -o bin/vcfcountalleles -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfafpath.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcflength.cpp -o bin/vcflength -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfafpath.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfdistance.cpp -o bin/vcfdistance -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfrandomsample.cpp -o bin/vcfrandomsample -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfentropy.cpp -o bin/vcfentropy -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfglxgt.cpp -o bin/vcfglxgt -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfroc.cpp -o bin/vcfroc -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfcheck.cpp -o bin/vcfcheck -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfstreamsort.cpp -o bin/vcfstreamsort -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/map:60,
from src/Variant.h:6,
from src/vcfroc.cpp:1:
/usr/include/c++/9/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::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++/9/bits/stl_tree.h:2452:7: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfuniq.cpp -o bin/vcfuniq -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfuniqalleles.cpp -o bin/vcfuniqalleles -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/map:61,
from src/Variant.h:6,
from src/vcfroc.cpp:1:
/usr/include/c++/9/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long 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++/9/bits/stl_map.h:499:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfremap.cpp -o bin/vcfremap -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfstreamsort.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' {aka '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcf2fasta.cpp -o bin/vcf2fasta -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfstreamsort.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfsitesummarize.cpp -o bin/vcfsitesummarize -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
/usr/include/c++/9/bits/stl_map.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type 'std::_Rb_tree<long 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/9/bits/stl_map.h:518:8: 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' {aka 'std::_Rb_tree_const_iterator<std::pair<const long double, std::vector<vcflib::VariantAllele*> > >'} changed in GCC 7.1
518 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfbreakmulti.cpp -o bin/vcfbreakmulti -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfcreatemulti.cpp -o bin/vcfcreatemulti -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfevenregions.cpp -o bin/vcfevenregions -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfcat.cpp -o bin/vcfcat -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfbreakmulti.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' {aka '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfgenosummarize.cpp -o bin/vcfgenosummarize -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfbreakmulti.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfgenosamplenames.cpp -o bin/vcfgenosamplenames -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfcreatemulti.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' {aka '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfgeno2haplo.cpp -o bin/vcfgeno2haplo -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfcreatemulti.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfleftalign.cpp -o bin/vcfleftalign -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfcombine.cpp -o bin/vcfcombine -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfgeno2alleles.cpp -o bin/vcfgeno2alleles -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfleftalign.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In function 'double entropy(const string&)':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfindex.cpp -o bin/vcfindex -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfgeno2haplo.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const vcflib::Variant&}; _Tp = vcflib::Variant; _Alloc = std::allocator<vcflib::Variant>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<vcflib::Variant>::iterator' {aka '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfgeno2haplo.cpp:1:
/usr/include/c++/9/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++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<vcflib::Variant*, std::vector<vcflib::Variant> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcf2dag.cpp -o bin/vcf2dag -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfsample2info.cpp -o bin/vcfsample2info -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfqual2info.cpp -o bin/vcfqual2info -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfinfo2qual.cpp -o bin/vcfinfo2qual -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfsample2info.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/queue:62,
from src/Variant.h:14,
from src/vcfsample2info.cpp:1:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/smithwaterman/SmithWatermanGotoh.h:4,
from src/Variant.h:21,
from src/vcfsample2info.cpp:1:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introselect(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1976 | __introselect(_RandomAccessIterator __first, _RandomAccessIterator __nth,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'double median(std::vector<double>&)':
/usr/include/c++/9/bits/stl_algo.h:4796:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4796 | std::__introselect(__first, __nth, __last,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
4797 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4798 | __gnu_cxx::__ops::__iter_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfsample2info.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfglbound.cpp -o bin/vcfglbound -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfunphase.cpp -o bin/vcfunphase -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfnull2ref.cpp -o bin/vcfnull2ref -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
g++ -Wdate-time -D_FORTIFY_SOURCE=2 src/vcfinfosummarize.cpp -o bin/vcfinfosummarize -I/usr/include/smithwaterman -I/usr/include/fastahack -Iinclude -Llib -lvcflib -Wl,-z,relro -Wl,-z,now -lz -lm -llzma -lbz2 -lssw -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -Ofast -D_FILE_OFFSET_BITS=64 -std=c++0x -DVERSION=\"1.0.1+dfsg-3+b5\" -ltabixpp -lhts -lsmithwaterman -ldisorder -lfastahack -lstdc++ -lm
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfglbound.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfglbound.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from src/Variant.h:4,
from src/vcfinfosummarize.cpp:1:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/queue:62,
from src/Variant.h:14,
from src/vcfinfosummarize.cpp:1:
/usr/include/c++/9/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_heap.h:214:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
214 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/9/algorithm:62,
from /usr/include/smithwaterman/SmithWatermanGotoh.h:4,
from src/Variant.h:21,
from src/vcfinfosummarize.cpp:1:
/usr/include/c++/9/bits/stl_algo.h: In function 'void std::__introselect(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]':
/usr/include/c++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1976 | __introselect(_RandomAccessIterator __first, _RandomAccessIterator __nth,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h:1976:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algo.h: In function 'double median(std::vector<double>&)':
/usr/include/c++/9/bits/stl_algo.h:4796:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4796 | std::__introselect(__first, __nth, __last,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
4797 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
4798 | __gnu_cxx::__ops::__iter_less_iter());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from src/Variant.h:4,
from src/vcfinfosummarize.cpp:1:
/usr/include/c++/9/bits/stl_vector.h: In function 'int main(int, char**)':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
cp -f scripts/* bin
make[2]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
markdown README.md > README.html
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
debian/rules override_dh_auto_test
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
export LD_LIBRARY_PATH=/<<BUILDDIR>>/libvcflib-1.0.1+dfsg/lib/:D_LIBRARY_PATH dh_auto_test
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch
dh_testroot -a
dh_prep -a
dh_auto_install -a
debian/rules override_dh_install
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+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-1.0.1+dfsg/debian/libvcflib-dev/usr/lib/arm-linux-gnueabihf/pkgconfig
mv libvcflib.pc /<<BUILDDIR>>/libvcflib-1.0.1+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-1.0.1+dfsg'
dh_installdocs -a
dh_installchangelogs -a
dh_installman -a
dh_lintian -a
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms
make[1]: Entering directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
dh_fixperms
chmod -x debian/*/usr/lib/R/site-library/*/*.R
make[1]: Leaving directory '/<<BUILDDIR>>/libvcflib-1.0.1+dfsg'
dh_missing -a
dh_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
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: 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/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/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/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/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/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/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/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/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/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/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/vcfnull2ref 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/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/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/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/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/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/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/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/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/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/vcfcheck 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/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/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/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/vcfcountalleles 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/vcfunphase 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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/vcfnormalizesvs 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/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/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/vcfclassify contains an unresolvable reference to symbol __aeabi_atexit@CXXABI_ARM_1.3.3: it's probably a plugin
dpkg-shlibdeps: warning: package could avoid a useless dependency if debian/libvcflib-tools/usr/lib/vcflib/bin/vcfecho debian/libvcflib-tools/usr/lib/vcflib/bin/vcfafpath debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremoveaberrantgenotypes debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2alleles debian/libvcflib-tools/usr/lib/vcflib/bin/vcfparsealts debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepgeno debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsample2info debian/libvcflib-tools/usr/lib/vcflib/bin/dumpContigsFromHeader debian/libvcflib-tools/usr/lib/vcflib/bin/iHS debian/libvcflib-tools/usr/lib/vcflib/bin/vcfaltcount debian/libvcflib-tools/usr/bin/vcfkeepinfo debian/libvcflib-tools/usr/lib/vcflib/bin/vcfnull2ref debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepsamples debian/libvcflib-tools/usr/lib/vcflib/bin/sequenceDiversity debian/libvcflib-tools/usr/lib/vcflib/bin/bFst debian/libvcflib-tools/usr/lib/vcflib/bin/vcfhethomratio debian/libvcflib-tools/usr/lib/vcflib/bin/vcfannotate debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcombine debian/libvcflib-tools/usr/lib/vcflib/bin/vcfqual2info debian/libvcflib-tools/usr/lib/vcflib/bin/vcfallelicprimitives debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniqalleles debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcleancomplex debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcheck debian/libvcflib-tools/usr/lib/vcflib/bin/genotypeSummary debian/libvcflib-tools/usr/lib/vcflib/bin/vcffilter debian/libvcflib-tools/usr/lib/vcflib/bin/vcfoverlay debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcreatemulti debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcountalleles debian/libvcflib-tools/usr/lib/vcflib/bin/vcfindex debian/libvcflib-tools/usr/lib/vcflib/bin/vcfleftalign debian/libvcflib-tools/usr/lib/vcflib/bin/pVst debian/libvcflib-tools/usr/lib/vcflib/bin/vcfentropy debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2tsv debian/libvcflib-tools/usr/lib/vcflib/bin/wcFst debian/libvcflib-tools/usr/lib/vcflib/bin/permuteSmooth debian/libvcflib-tools/usr/bin/vcffilter debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcat debian/libvcflib-tools/usr/lib/vcflib/bin/vcfnumalt debian/libvcflib-tools/usr/lib/vcflib/bin/vcfinfo2qual debian/libvcflib-tools/usr/lib/vcflib/bin/vcfcommonsamples debian/libvcflib-tools/usr/lib/vcflib/bin/vcfprimers debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2dag debian/libvcflib-tools/usr/lib/vcflib/bin/segmentIhs debian/libvcflib-tools/usr/lib/vcflib/bin/vcfglbound debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplenames debian/libvcflib-tools/usr/lib/vcflib/bin/pFst debian/libvcflib-tools/usr/lib/vcflib/bin/vcfrandom debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenosamplenames debian/libvcflib-tools/usr/lib/vcflib/bin/vcfunphase debian/libvcflib-tools/usr/lib/vcflib/bin/vcflength debian/libvcflib-tools/usr/lib/vcflib/bin/vcf2fasta debian/libvcflib-tools/usr/lib/vcflib/bin/meltEHH debian/libvcflib-tools/usr/lib/vcflib/bin/vcfkeepinfo debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstats debian/libvcflib-tools/usr/bin/vcf2tsv debian/libvcflib-tools/usr/lib/vcflib/bin/vcfflatten debian/libvcflib-tools/usr/lib/vcflib/bin/vcfglxgt debian/libvcflib-tools/usr/lib/vcflib/bin/vcfld debian/libvcflib-tools/usr/lib/vcflib/bin/vcfrandomsample debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremap debian/libvcflib-tools/usr/lib/vcflib/bin/vcfdistance debian/libvcflib-tools/usr/lib/vcflib/bin/vcfinfosummarize debian/libvcflib-tools/usr/lib/vcflib/bin/smoother debian/libvcflib-tools/usr/lib/vcflib/bin/vcfhetcount debian/libvcflib-tools/usr/lib/vcflib/bin/vcfevenregions debian/libvcflib-tools/usr/lib/vcflib/bin/vcfintersect debian/libvcflib-tools/usr/lib/vcflib/bin/popStats debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsamplediff debian/libvcflib-tools/usr/lib/vcflib/bin/plotHaps debian/libvcflib-tools/usr/lib/vcflib/bin/normalize-iHS debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenosummarize debian/libvcflib-tools/usr/lib/vcflib/bin/vcfaddinfo debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenotypes debian/libvcflib-tools/usr/lib/vcflib/bin/vcfbreakmulti debian/libvcflib-tools/usr/lib/vcflib/bin/vcfroc debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgenotypecompare debian/libvcflib-tools/usr/lib/vcflib/bin/hapLrt debian/libvcflib-tools/usr/lib/vcflib/bin/vcfannotategenotypes debian/libvcflib-tools/usr/lib/vcflib/bin/vcfstreamsort debian/libvcflib-tools/usr/lib/vcflib/bin/vcfsitesummarize debian/libvcflib-tools/usr/lib/vcflib/bin/abba-baba debian/libvcflib-tools/usr/lib/vcflib/bin/permuteGPAT++ debian/libvcflib-tools/usr/lib/vcflib/bin/vcffixup debian/libvcflib-tools/usr/lib/vcflib/bin/vcfuniq debian/libvcflib-tools/usr/lib/vcflib/bin/vcfnormalizesvs debian/libvcflib-tools/usr/lib/vcflib/bin/vcfgeno2haplo debian/libvcflib-tools/usr/lib/vcflib/bin/segmentFst debian/libvcflib-tools/usr/lib/vcflib/bin/vcfremovesamples debian/libvcflib-tools/usr/lib/vcflib/bin/vcfclassify were not linked against ld-linux-armhf.so.3 (they use none of the library's symbols)
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'libvcflib1' in '../libvcflib1_1.0.1+dfsg-3+b5_armhf.deb'.
dpkg-deb: building package 'libvcflib-dev' in '../libvcflib-dev_1.0.1+dfsg-3+b5_armhf.deb'.
dpkg-deb: building package 'libvcflib-tools-dbgsym' in '../libvcflib-tools-dbgsym_1.0.1+dfsg-3+b5_armhf.deb'.
dpkg-deb: building package 'libvcflib-tools' in '../libvcflib-tools_1.0.1+dfsg-3+b5_armhf.deb'.
dpkg-deb: building package 'libvcflib1-dbgsym' in '../libvcflib1-dbgsym_1.0.1+dfsg-3+b5_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../libvcflib_1.0.1+dfsg-3+b5_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-05-30T20:45:36Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
libvcflib_1.0.1+dfsg-3+b5_armhf.changes:
----------------------------------------
Format: 1.8
Date: Wed, 12 Feb 2020 13:00:17 +0100
Source: libvcflib (1.0.1+dfsg-3)
Binary: libvcflib-dev libvcflib-tools libvcflib-tools-dbgsym libvcflib1 libvcflib1-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 1.0.1+dfsg-3+b5
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.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 (1.0.1+dfsg-3+b5) bullseye-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
Checksums-Sha1:
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5967a63f997064fcf92ed105e1dbe090 513284 science optional libvcflib-tools_1.0.1+dfsg-3+b5_armhf.deb
31f3cd251ae7bdf0842a392b211f1e6e 1416908 debug optional libvcflib1-dbgsym_1.0.1+dfsg-3+b5_armhf.deb
49af1c581082b0fc95789a3442fa6dd3 126544 libs optional libvcflib1_1.0.1+dfsg-3+b5_armhf.deb
910a5580dcd45228f55d4f6247df4ec3 7213 science optional libvcflib_1.0.1+dfsg-3+b5_armhf.buildinfo
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
libvcflib-dev_1.0.1+dfsg-3+b5_armhf.deb
---------------------------------------
new Debian package, version 2.0.
size 28936 bytes: control archive=1512 bytes.
1289 bytes, 27 lines control
1188 bytes, 17 lines md5sums
Package: libvcflib-dev
Source: libvcflib (1.0.1+dfsg-3)
Version: 1.0.1+dfsg-3+b5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 171
Depends: libvcflib1 (= 1.0.1+dfsg-3+b5), 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 2020-02-12 12:00 ./
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/include/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/include/intervaltree/
-rw-r--r-- root/root 11699 2020-02-12 12:00 ./usr/include/intervaltree/IntervalTree.h
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/include/vcflib/
-rw-r--r-- root/root 5601 2020-02-12 12:00 ./usr/include/vcflib/BedReader.h
-rw-r--r-- root/root 22615 2020-02-12 12:00 ./usr/include/vcflib/Variant.h
-rw-r--r-- root/root 470 2020-02-12 12:00 ./usr/include/vcflib/convert.h
-rw-r--r-- root/root 1777 2019-10-01 07:06 ./usr/include/vcflib/filevercmp.h
-rw-r--r-- root/root 1011 2020-02-12 12:00 ./usr/include/vcflib/join.h
-rw-r--r-- root/root 6353 2020-02-12 12:00 ./usr/include/vcflib/mt19937ar.h
-rw-r--r-- root/root 2155 2020-02-12 12:00 ./usr/include/vcflib/multichoose.h
-rw-r--r-- root/root 3446 2020-02-12 12:00 ./usr/include/vcflib/multipermute.h
-rw-r--r-- root/root 1598 2020-02-12 12:00 ./usr/include/vcflib/split.h
-rw-r--r-- root/root 75369 2020-02-12 12:00 ./usr/include/vcflib/vec128int.h
-rw-r--r-- root/root 13921 2020-02-12 12:00 ./usr/include/vcflib/veclib_types.h
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/arm-linux-gnueabihf/
lrwxrwxrwx root/root 0 2020-02-12 12:00 ./usr/lib/arm-linux-gnueabihf/libvcflib.so -> libvcflib.so.1
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/arm-linux-gnueabihf/pkgconfig/
-rw-r--r-- root/root 283 2020-02-12 12:00 ./usr/lib/arm-linux-gnueabihf/pkgconfig/libvcflib.pc
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/doc/libvcflib-dev/
-rw-r--r-- root/root 227 2020-02-12 12:00 ./usr/share/doc/libvcflib-dev/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1586 2020-02-12 12:00 ./usr/share/doc/libvcflib-dev/changelog.Debian.gz
-rw-r--r-- root/root 2042 2019-12-10 11:44 ./usr/share/doc/libvcflib-dev/copyright
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/lintian/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 91 2019-12-10 11:34 ./usr/share/lintian/overrides/libvcflib-dev
libvcflib-tools-dbgsym_1.0.1+dfsg-3+b5_armhf.deb
------------------------------------------------
new Debian package, version 2.0.
size 13886732 bytes: control archive=4412 bytes.
3914 bytes, 12 lines control
9211 bytes, 87 lines md5sums
Package: libvcflib-tools-dbgsym
Source: libvcflib (1.0.1+dfsg-3)
Version: 1.0.1+dfsg-3+b5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 14957
Depends: libvcflib-tools (= 1.0.1+dfsg-3+b5)
Section: debug
Priority: optional
Description: debug symbols for libvcflib-tools
Build-Ids: 083f03ac5ca1b44f3029df8b877fbfaee1b1dba9 0846c7f4c73cd90b797085a92c09aa0445b4b6e7 0904b9d07cb8ae1ceb2b94b61d0cfc05373d092f 0bb666994b68d5f44508f894559e64ce68cb97b3 0ddebdd16c41de309e3535ff3c32e00ddf52a220 13e3ed9e6572bdd4f29bb48f28defe47951b9d3c 1771b025b68f79cdb896a2ea9d0aa5c884b200a7 1eec119a3320e0fd3f03909fbcf89fa4a654b3ca 21ed78ef78ca6419825b43d1d94b87f54340fe61 22bb83ed6fbc6dda79d743bd2d6fc8a1d79f333d 2422ed3e2d931e2f676ad3cdf1e9a5ef3b8b092a 248c4fcced8ca4ad0637354549e7904b84cd0c9b 285d436b15ef91d8d46c032469b5dcb087295b08 2aedb2d644271a8de187ae5d9fca529a6176c458 2b24330ce45a5e444cad58b1c5b78d8cc8cd2618 2cd9afbc086ce3c501f1c44819ac629534a9f975 2fb52ce208bdd307d053a88a3f8fc4da7c8908cd 334a69b779eaee2278509b002791331bc5c84b5b 34db7ae270a12b919b593c0fb5e8154bcccde13a 3b7b623e8f063a344e7efbb5fa588e74b23a109c 3c6fad470054ea1407809d4b330be91716e843f0 3d3e0b2f646a2df9537eae246e62849d539b7082 41cb5c85a2f07c29fdff82edf84e4c5bcba90225 43e617159d65897021de8bd8e72d6c60c4d13fc8 48a053d74fe3eb6fd49e4e8b3c1b2f0ba6a7e31b 4be609ea2387d15125a08201bba2518ecea5b2f7 4d14f0c7e755a809bf2d8d570a6ecae915579cd1 54762aaefcac1fd1e52c60bd6b42bb003325806c 561f73deeef3c6239240f0d101e47aaba52c5281 5b65f74610e467aa6ba161cf53768a9534872f26 610398e03ddc9bab476f98f66a980747a7ff54cf 616d63de7fc6ab2c9ab302fd8b43dcf0f26460ec 62cac2f741294e286cc30f0eda416308bc12b0c8 644cbfb130f0aaa43c2c7d255ea498a963415844 6476f016196f55810b4a7c75b6a3d94ca699c4ca 666a5d8ab5bf3ebdb972decddf5ca0a261690d82 6794d20dde00f549734a6f329dc49d79f6b783f5 6e63e26a8634c143c33a7abe0cbc78a3983159b9 6edacf65cce06fcdc74aabb87c7ac39266521a21 71de80b7ff11050dd6f611abf49017513e7aadb4 722ce5ef877d1950281663ada26e09e1c66f9911 72462088e8ad91abc339092933cf5d0ec1fc87b7 7cf3e89035402e4509e64c7a644c5ac207000fc8 7d2b93a02b4f53a002ae1c8041c25a5292e5ce2a 83f1282936293eb469289e460f72cb5f9758a006 85012c012086eadc0b38c5fa7d546e6a1cbb789e 8aa437c3665dbbaf22284c7179d2ca350569c149 8ecbb3279ab117e67ed50bde535ff8008da970db 8fd26343b40bfe25adb35cef1fe34bd393f609d7 9042b18a8db64ec5166dc0ede2bd4792f73a89b0 94c985b057339d49b4f83e6b669a1d27225ee961 95e954c10477d0eb1e5d77b24d82012a0968e6ff 96fdab462a8eaa652eca451b6858cbd20fb8ca1b a02f124607bc962d2d0bb9bb20321cb5a91575e8 a22f8f40edb013cdb775be92cf5fb8a4b5d8139b a2fed7df137a56ba405b411a8bd8ad76a42014a2 a578ae2eba6a594426ef1c91172f4f0e2d1489af a8e73b788dd472ca31dfce30249c54d52290f041 a9f656aa1dff39b7dea751bca42fa1af0b5b1f63 b21bab396412de71248b7878d6845a6baf2adc82 b476f66b8fdf87a12f192a18c390f0550156d649 b64625e299db2a5ffd3e29bd6411a4d679f53888 ba3e9664dd702256d265a932c6517662a195e7bc c171f1c95636ae0fa0e52182474d6684a42ac43d c816b57e99c060e043db7eba376cd8eb838b626a c9d3ac073113cb39cb4d4994959bac0011aba05e ca3b89793b00967b274b3b799f6ab61e5cb7fc71 cc90f8c683d40d1477818734fd14d274d0138107 d5eac90b5b3865f4b66417c7a5789aae0acc253f de6eed8d26fb05781ab0a5e8582f5a94da386807 e0cffa2e53f81162752c11dcd171aa7abe869042 e304c4204cbe96192677db14098ffbbb7d595754 e3085327385ba0ba672d2838cf7764fe0440fdc0 e4d8cee5429cd186f81375e83ef319805049b800 e607eed9ee928f9df94160f5a50843b6a66141b7 e63f63cfaf2fabc1d3326e9a284b685fa7e868d6 e64492a0bbaf89557d72711878c3bc5432a626f3 e6836f47f61692842487cc602ca4943f96e862cd eb4ece4832ef5256ebc7d44defdd74e886853538 ec3263016ea31078304659e89392ffc51e2475b9 ec7de68e5579897bf5a6da18d373fc50b93e6f65 f0cd836d876b869268c31d7857c943522202f2f4 f171ef06a47bc9e00ca249fb1d342c8eb79daf3e f2846a1415594338f465f440eafe4d2583321d0e f81c496234a26f85d72db10c91c9cc66e420aa51 fff18d021922b73f07ff8681f1030f5db4323313
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libvcflib-tools_1.0.1+dfsg-3+b5_armhf.deb
-----------------------------------------
new Debian package, version 2.0.
size 513284 bytes: control archive=4644 bytes.
1545 bytes, 29 lines control
9310 bytes, 139 lines md5sums
Package: libvcflib-tools
Source: libvcflib (1.0.1+dfsg-3)
Version: 1.0.1+dfsg-3+b5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 3138
Depends: libc6 (>= 2.15), libdisorder0 (>= 0.0.2), libfastahack0 (>= 1.0.0+dfsg), libgcc-s1 (>= 3.5), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 9), libtabixpp0 (>= 1.0.0), libvcflib1 (>= 1.0.1+dfsg), perl:any, 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 83 2020-02-12 12:00 ./usr/lib/vcflib/bin/vcfsort
-rwxr-xr-x root/root 59192 2020-02-12 12:00 ./usr/lib/vcflib/bin/vcfstats
-rwxr-xr-x root/root 46808 2020-02-12 12:00 ./usr/lib/vcflib/bin/vcfstreamsort
-rwxr-xr-x root/root 18072 2020-02-12 12:00 ./usr/lib/vcflib/bin/vcfuniq
-rwxr-xr-x root/root 22168 2020-02-12 12:00 ./usr/lib/vcflib/bin/vcfuniqalleles
-rwxr-xr-x root/root 22168 2020-02-12 12:00 ./usr/lib/vcflib/bin/vcfunphase
-rwxr-xr-x root/root 5459 2020-02-12 12:00 ./usr/lib/vcflib/bin/vcfvarstats
-rwxr-xr-x root/root 42648 2020-02-12 12:00 ./usr/lib/vcflib/bin/wcFst
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/doc/libvcflib-tools/
-rw-r--r-- root/root 227 2020-02-12 12:00 ./usr/share/doc/libvcflib-tools/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1586 2020-02-12 12:00 ./usr/share/doc/libvcflib-tools/changelog.Debian.gz
-rw-r--r-- root/root 2042 2019-12-10 11:44 ./usr/share/doc/libvcflib-tools/copyright
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/lintian/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 93 2019-12-10 11:34 ./usr/share/lintian/overrides/libvcflib-tools
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/man/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/man/man1/
-rw-r--r-- root/root 505 2020-02-12 12:00 ./usr/share/man/man1/vcflib.1.gz
libvcflib1-dbgsym_1.0.1+dfsg-3+b5_armhf.deb
-------------------------------------------
new Debian package, version 2.0.
size 1416908 bytes: control archive=564 bytes.
430 bytes, 13 lines control
106 bytes, 1 lines md5sums
Package: libvcflib1-dbgsym
Source: libvcflib (1.0.1+dfsg-3)
Version: 1.0.1+dfsg-3+b5
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 1473
Depends: libvcflib1 (= 1.0.1+dfsg-3+b5)
Section: debug
Priority: optional
Multi-Arch: same
Description: debug symbols for libvcflib1
Build-Ids: 7c20ee2258f0b9265e62814cb81a85eb13b91d17
drwxr-xr-x root/root 0 2020-02-12 12:00 ./
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/debug/.build-id/7c/
-rw-r--r-- root/root 1497684 2020-02-12 12:00 ./usr/lib/debug/.build-id/7c/20ee2258f0b9265e62814cb81a85eb13b91d17.debug
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-02-12 12:00 ./usr/share/doc/libvcflib1-dbgsym -> libvcflib1
libvcflib1_1.0.1+dfsg-3+b5_armhf.deb
------------------------------------
new Debian package, version 2.0.
size 126544 bytes: control archive=1252 bytes.
1268 bytes, 25 lines control
383 bytes, 5 lines md5sums
39 bytes, 1 lines shlibs
65 bytes, 2 lines triggers
Package: libvcflib1
Source: libvcflib (1.0.1+dfsg-3)
Version: 1.0.1+dfsg-3+b5
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 341
Depends: libc6 (>= 2.15), libdisorder0 (>= 0.0.2), libfastahack0 (>= 1.0.0+dfsg), libgcc-s1 (>= 3.5), libsmithwaterman0 (>= 0.0+git20160702.2610e25), libstdc++6 (>= 9), 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 2020-02-12 12:00 ./
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/lib/arm-linux-gnueabihf/
-rw-r--r-- root/root 329924 2020-02-12 12:00 ./usr/lib/arm-linux-gnueabihf/libvcflib.so.1
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/doc/libvcflib1/
-rw-r--r-- root/root 227 2020-02-12 12:00 ./usr/share/doc/libvcflib1/changelog.Debian.armhf.gz
-rw-r--r-- root/root 1586 2020-02-12 12:00 ./usr/share/doc/libvcflib1/changelog.Debian.gz
-rw-r--r-- root/root 2042 2019-12-10 11:44 ./usr/share/doc/libvcflib1/copyright
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/lintian/
drwxr-xr-x root/root 0 2020-02-12 12:00 ./usr/share/lintian/overrides/
-rw-r--r-- root/root 88 2019-12-10 11:34 ./usr/share/lintian/overrides/libvcflib1
+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 200544
Build-Time: 1205
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 429
Job: libvcflib_1.0.1+dfsg-3
Machine Architecture: armhf
Package: libvcflib
Package-Time: 1691
Source-Version: 1.0.1+dfsg-3
Space: 200544
Status: successful
Version: 1.0.1+dfsg-3+b5
--------------------------------------------------------------------------------
Finished at 2020-05-30T20:45:36Z
Build needed 00:28:11, 200544k disc space