bali-phy →
3.4.1+dfsg-2 →
armhf → 2019-07-10 05:55:09
sbuild (Debian sbuild) 0.72.0 (25 Oct 2016) on mb-lxc-01
+==============================================================================+
| bali-phy 3.4.1+dfsg-2 (armhf) Wed, 10 Jul 2019 05:33:08 +0000 |
+==============================================================================+
Package: bali-phy
Version: 3.4.1+dfsg-2
Source Version: 3.4.1+dfsg-2
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-f130a75c-b13a-4a18-9951-e9edeaa7167f' 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 [11.4 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.0 MB]
Fetched 24.4 MB in 13s (1930 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: 'bali-phy' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/bali-phy.git
Please use:
git clone https://salsa.debian.org/med-team/bali-phy.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 1306 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main bali-phy 3.4.1+dfsg-2 (dsc) [2179 B]
Get:2 http://172.17.0.1/private bullseye-staging/main bali-phy 3.4.1+dfsg-2 (tar) [1301 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main bali-phy 3.4.1+dfsg-2 (diff) [3172 B]
Fetched 1306 kB in 2s (694 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/bali-phy-KXzWDG/bali-phy-3.4.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/bali-phy-KXzWDG' 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-ycQzX2/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-ycQzX2/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-ycQzX2/gpg/trustdb.gpg: trustdb created
gpg: key 37145E60F90AF620: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 37145E60F90AF620: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 37145E60F90AF620: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ Packages [434 B]
Fetched 2110 B in 0s (10.3 kB/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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 5 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ycQzX2/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 (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12050 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11), meson (>= 0.45), libcairo2-dev, libeigen3-dev, nlohmann-json3-dev, pandoc, libboost-dev, libboost-program-options-dev, libboost-random-dev, libboost-system-dev, libboost-filesystem-dev, libboost-chrono-dev
Filtered Build-Depends: debhelper (>= 11), meson (>= 0.45), libcairo2-dev, libeigen3-dev, nlohmann-json3-dev, pandoc, libboost-dev, libboost-program-options-dev, libboost-random-dev, libboost-system-dev, libboost-filesystem-dev, libboost-chrono-dev
dpkg-deb: building package 'sbuild-build-depends-bali-phy-dummy' in '/<<BUILDDIR>>/resolver-ycQzX2/apt_archive/sbuild-build-depends-bali-phy-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-bali-phy-dummy sbuild-build-depends-core-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-ycQzX2/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ Sources [574 B]
Get:5 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ Packages [656 B]
Fetched 2563 B in 0s (12.1 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install bali-phy build dependencies (apt-based resolver)
--------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libblkid-dev libboost-chrono-dev libboost-chrono1.67-dev
libboost-chrono1.67.0 libboost-dev libboost-filesystem-dev
libboost-filesystem1.67-dev libboost-filesystem1.67.0
libboost-program-options-dev libboost-program-options1.67-dev
libboost-program-options1.67.0 libboost-random-dev libboost-random1.67-dev
libboost-random1.67.0 libboost-system-dev libboost-system1.67-dev
libboost-system1.67.0 libboost1.67-dev libbsd0 libcairo-gobject2
libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 libeigen3-dev
libelf1 libexpat1 libexpat1-dev libffi-dev libfile-stripnondeterminism-perl
libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libglib2.0-0
libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libice-dev
libice6 libicu63 liblua5.1-0 liblzo2-2 libmagic-mgc libmagic1 libmount-dev
libmpdec2 libncurses6 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpng16-16
libpthread-stubs0-dev libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib libselinux1-dev libsepol1-dev libsigsegv2 libsm-dev
libsm6 libssl1.1 libtinfo5 libtool libuchardet0 libx11-6 libx11-data
libx11-dev libxau-dev libxau6 libxcb-render0 libxcb-render0-dev libxcb-shm0
libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev
libxext6 libxml2 libxrender-dev libxrender1 libyaml-0-2 m4 man-db meson
mime-support ninja-build nlohmann-json3-dev pandoc pandoc-data pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3-pkg-resources python3.7 python3.7-minimal sensible-utils ucf
uuid-dev x11-common x11proto-core-dev x11proto-dev x11proto-xext-dev
xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff
libboost-doc libboost1.67-doc libboost-atomic1.67-dev
libboost-container1.67-dev libboost-context1.67-dev
libboost-coroutine1.67-dev libboost-date-time1.67-dev
libboost-exception1.67-dev libboost-fiber1.67-dev libboost-graph1.67-dev
libboost-graph-parallel1.67-dev libboost-iostreams1.67-dev
libboost-locale1.67-dev libboost-log1.67-dev libboost-math1.67-dev
libboost-mpi1.67-dev libboost-mpi-python1.67-dev libboost-numpy1.67-dev
libboost-python1.67-dev libboost-regex1.67-dev
libboost-serialization1.67-dev libboost-signals1.67-dev
libboost-stacktrace1.67-dev libboost-test1.67-dev libboost-thread1.67-dev
libboost-timer1.67-dev libboost-type-erasure1.67-dev libboost-wave1.67-dev
libboost1.67-tools-dev libmpfrc++-dev libntl-dev libcairo2-doc libeigen3-doc
libglib2.0-doc libgdk-pixbuf2.0-bin | libgdk-pixbuf2.0-dev libxml2-utils
libice-doc libsm-doc libtool-doc gfortran | fortran95-compiler gcj-jdk
libx11-doc libxcb-doc libxext-doc m4-doc apparmor less www-browser
texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc
texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python
ruby r-base-core libjs-mathjax node-katex libmail-box-perl python3-doc
python3-tk python3-venv python3-setuptools python3.7-venv python3.7-doc
binfmt-support
Recommended packages:
curl | wget | lynx libarchive-cpio-perl freetype2-doc shared-mime-info
xdg-user-dirs libgpm2 libpng-tools libltdl-dev libmail-sendmail-perl
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-strip-nondeterminism dwz file fontconfig-config
fonts-dejavu-core gettext gettext-base groff-base intltool-debian
libarchive-zip-perl libblkid-dev libboost-chrono-dev libboost-chrono1.67-dev
libboost-chrono1.67.0 libboost-dev libboost-filesystem-dev
libboost-filesystem1.67-dev libboost-filesystem1.67.0
libboost-program-options-dev libboost-program-options1.67-dev
libboost-program-options1.67.0 libboost-random-dev libboost-random1.67-dev
libboost-random1.67.0 libboost-system-dev libboost-system1.67-dev
libboost-system1.67.0 libboost1.67-dev libbsd0 libcairo-gobject2
libcairo-script-interpreter2 libcairo2 libcairo2-dev libcroco3 libeigen3-dev
libelf1 libexpat1 libexpat1-dev libffi-dev libfile-stripnondeterminism-perl
libfontconfig1 libfontconfig1-dev libfreetype6 libfreetype6-dev libglib2.0-0
libglib2.0-bin libglib2.0-data libglib2.0-dev libglib2.0-dev-bin libice-dev
libice6 libicu63 liblua5.1-0 liblzo2-2 libmagic-mgc libmagic1 libmount-dev
libmpdec2 libncurses6 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5
libpipeline1 libpixman-1-0 libpixman-1-dev libpng-dev libpng16-16
libpthread-stubs0-dev libpython3-stdlib libpython3.7-minimal
libpython3.7-stdlib libselinux1-dev libsepol1-dev libsigsegv2 libsm-dev
libsm6 libssl1.1 libtinfo5 libtool libuchardet0 libx11-6 libx11-data
libx11-dev libxau-dev libxau6 libxcb-render0 libxcb-render0-dev libxcb-shm0
libxcb-shm0-dev libxcb1 libxcb1-dev libxdmcp-dev libxdmcp6 libxext-dev
libxext6 libxml2 libxrender-dev libxrender1 libyaml-0-2 m4 man-db meson
mime-support ninja-build nlohmann-json3-dev pandoc pandoc-data pkg-config
po-debconf python3 python3-distutils python3-lib2to3 python3-minimal
python3-pkg-resources python3.7 python3.7-minimal
sbuild-build-depends-bali-phy-dummy sensible-utils ucf uuid-dev x11-common
x11proto-core-dev x11proto-dev x11proto-xext-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
0 upgraded, 135 newly installed, 0 to remove and 5 not upgraded.
Need to get 70.7 MB of archives.
After this operation, 447 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-ycQzX2/apt_archive ./ sbuild-build-depends-bali-phy-dummy 0.invalid.0 [940 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.9.1-2 [104 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20181013-2 [309 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 1.22.4-3 [782 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.1-2 [26.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.8.5-2 [1230 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1c-1 [1259 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.3-2 [583 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.6-2 [77.1 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.3-2 [1464 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.62 [37.2 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.3-2 [1664 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.3-2 [330 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.3-1 [61.5 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12 [15.8 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.35-4 [242 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.35-4 [110 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.35-4 [65.3 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-9 [117 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-2 [185 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-9 [434 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-9 [547 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.12-3 [66.0 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.58.3-2 [1077 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-7+b1 [570 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.12-3 [132 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.1+20181013-2 [78.6 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-9 [1219 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.1.1 [1016 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf uuid-dev armhf 2.33.1-0.1 [92.4 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libblkid-dev armhf 2.33.1-0.1 [210 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libboost1.67-dev armhf 1.67.0-13 [8386 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libboost-system1.67.0 armhf 1.67.0-13 [228 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libboost-chrono1.67.0 armhf 1.67.0-13 [231 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libboost-chrono1.67-dev armhf 1.67.0-13 [233 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libboost-chrono-dev armhf 1.67.0.1+b1 [4548 B]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.67.0.1+b1 [4140 B]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem1.67.0 armhf 1.67.0-13 [254 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf libboost-system1.67-dev armhf 1.67.0-13 [230 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem1.67-dev armhf 1.67.0-13 [259 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf libboost-filesystem-dev armhf 1.67.0.1+b1 [3960 B]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.67.0 armhf 1.67.0-13 [330 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options1.67-dev armhf 1.67.0-13 [374 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libboost-program-options-dev armhf 1.67.0.1+b1 [3940 B]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libboost-random1.67.0 armhf 1.67.0-13 [230 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libboost-random1.67-dev armhf 1.67.0-13 [230 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libboost-random-dev armhf 1.67.0.1+b1 [3920 B]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libboost-system-dev armhf 1.67.0.1+b1 [4060 B]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.36-6 [273 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.9.1-3 [318 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.7-1 [298 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.7-1 [689 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.13.1-2 [99.3 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libcairo-gobject2 armhf 1.16.0-4 [123 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf liblzo2-2 armhf 2.10-0.1 [48.4 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libcairo-script-interpreter2 armhf 1.16.0-4 [150 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.6-2 [127 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-1 [206 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libpng-dev armhf 1.6.36-6 [281 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6-dev armhf 2.9.1-3 [479 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1-dev armhf 2.13.1-2 [943 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1 [21.9 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2018.4-4 [251 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf x11proto-core-dev all 2018.4-4 [3128 B]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.8-1+b2 [22.4 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.3.5-1 [100 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.13.1-2 [169 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.6.7-1 [760 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libxrender-dev armhf 1:0.9.10-1 [37.7 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf x11proto-xext-dev all 2018.4-4 [3128 B]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libxext-dev armhf 2:1.3.3-1+b2 [102 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf x11-common all 1:7.7+19 [251 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libice6 armhf 2:1.0.9-2 [51.6 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libsm6 armhf 2:1.2.3-1 [32.9 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libice-dev armhf 2:1.0.9-2 [58.8 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libsm-dev armhf 2:1.2.3-1 [35.4 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-dev armhf 0.36.0-1 [477 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0-dev armhf 1.13.1-2 [111 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0-dev armhf 1.13.1-2 [100 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libffi-dev armhf 3.2.1-9 [159 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-data all 2.58.3-2 [1109 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-bin armhf 2.58.3-2 [117 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.7.3-1 [76.7 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.7.3-1 [142 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-dev-bin armhf 2.58.3-2 [154 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf libmount-dev armhf 2.33.1-0.1 [209 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libpcre16-3 armhf 2:8.39-12 [234 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf libpcre32-3 armhf 2:8.39-12 [227 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf libpcrecpp0v5 armhf 2:8.39-12 [150 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libpcre3-dev armhf 2:8.39-12 [564 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libsepol1-dev armhf 2.8-1 [309 kB]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf libselinux1-dev armhf 2.8-1+b1 [156 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-dev armhf 2.58.3-2 [1372 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libcairo2-dev armhf 1.16.0-4 [619 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libeigen3-dev all 3.3.7-1 [850 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf liblua5.1-0 armhf 5.1.5-8.1 [83.3 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libyaml-0-2 armhf 0.2.1-1 [38.8 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf ninja-build armhf 1.8.2-1 [78.8 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 41.0.1-1 [154 kB]
Get:132 http://172.17.0.1/private bullseye-staging/main armhf meson all 0.49.2-1 [281 kB]
Get:133 http://172.17.0.1/private bullseye-staging/main armhf nlohmann-json3-dev all 3.5.0-0.1 [681 kB]
Get:134 http://172.17.0.1/private bullseye-staging/main armhf pandoc-data all 2.2.1-3 [329 kB]
Get:135 http://172.17.0.1/private bullseye-staging/main armhf pandoc armhf 2.2.1-3+b2 [17.5 MB]
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No schema files found: doing nothing.
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update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults
invoke-rc.d: could not determine current runlevel
invoke-rc.d: policy-rc.d denied execution of start.
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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
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Setting up libmount-dev:armhf (2.33.1-0.1) ...
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Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.3-2) ...
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Setting up libxext6:armhf (2:1.3.3-1+b2) ...
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Setting up python3 (3.7.3-1) ...
Setting up man-db (2.8.5-2) ...
Not building database; man-db/auto-update is not 'true'.
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Setting up libcairo-gobject2:armhf (1.16.0-4) ...
Setting up libcairo-script-interpreter2:armhf (1.16.0-4) ...
Setting up libcairo2-dev:armhf (1.16.0-4) ...
Setting up dh-autoreconf (19) ...
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Setting up sbuild-build-depends-bali-phy-dummy (0.invalid.0) ...
Setting up dh-strip-nondeterminism (1.1.2-1) ...
Processing triggers for libc-bin (2.28-10+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.4.0-124-generic armhf (armv8l)
Toolchain package versions: binutils_2.31.1-16+rpi1 dpkg-dev_1.19.7 g++-8_8.3.0-6+rpi1 gcc-8_8.3.0-6+rpi1 libc6-dev_2.28-10+rpi1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 linux-libc-dev_4.18.20-2+rpi1
Package versions: adduser_3.118 apt_1.8.2 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-9 autotools-dev_20180224.1 base-files_10.3+rpi1 base-passwd_3.5.46 bash_5.0-4 binutils_2.31.1-16+rpi1 binutils-arm-linux-gnueabihf_2.31.1-16+rpi1 binutils-common_2.31.1-16+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.33.1-0.1 build-essential_12.6 bzip2_1.0.6-9.1 coreutils_8.30-3 cpp_4:8.3.0-1+rpi2 cpp-8_8.3.0-6+rpi1 dash_0.5.10.2-5 debconf_1.5.71 debhelper_12.1.1 debianutils_4.8.6.1 dh-autoreconf_19 dh-strip-nondeterminism_1.1.2-1 diffutils_1:3.7-3 dirmngr_2.2.12-1+rpi1 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.12-3 e2fsprogs_1.44.5-1 fakeroot_1.23-1 fdisk_2.33.1-0.1 file_1:5.35-4 findutils_4.6.0+git+20190209-2 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:8.3.0-1+rpi2 g++-8_8.3.0-6+rpi1 gcc_4:8.3.0-1+rpi2 gcc-4.9-base_4.9.4-2+rpi1+b19 gcc-5-base_5.5.0-8 gcc-6-base_6.5.0-1+rpi1+b1 gcc-7-base_7.3.0-19 gcc-8_8.3.0-6+rpi1 gcc-8-base_8.3.0-6+rpi1 gettext_0.19.8.1-9 gettext-base_0.19.8.1-9 gnupg_2.2.12-1+rpi1 gnupg-l10n_2.2.12-1+rpi1 gnupg-utils_2.2.12-1+rpi1 gpg_2.2.12-1+rpi1 gpg-agent_2.2.12-1+rpi1 gpg-wks-client_2.2.12-1+rpi1 gpg-wks-server_2.2.12-1+rpi1 gpgconf_2.2.12-1+rpi1 gpgsm_2.2.12-1+rpi1 gpgv_2.2.12-1+rpi1 grep_3.3-1 groff-base_1.22.4-3 gzip_1.9-3 hostname_3.21 init-system-helpers_1.56+nmu1 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-4 libapt-pkg5.0_1.8.2 libarchive-zip-perl_1.64-1 libasan5_8.3.0-6+rpi1 libassuan0_2.5.2-1 libatomic1_8.3.0-6+rpi1 libattr1_1:2.4.48-4 libaudit-common_1:2.8.4-3 libaudit1_1:2.8.4-3 libbinutils_2.31.1-16+rpi1 libblkid-dev_2.33.1-0.1 libblkid1_2.33.1-0.1 libboost-chrono-dev_1.67.0.1+b1 libboost-chrono1.67-dev_1.67.0-13 libboost-chrono1.67.0_1.67.0-13 libboost-dev_1.67.0.1+b1 libboost-filesystem-dev_1.67.0.1+b1 libboost-filesystem1.67-dev_1.67.0-13 libboost-filesystem1.67.0_1.67.0-13 libboost-program-options-dev_1.67.0.1+b1 libboost-program-options1.67-dev_1.67.0-13 libboost-program-options1.67.0_1.67.0-13 libboost-random-dev_1.67.0.1+b1 libboost-random1.67-dev_1.67.0-13 libboost-random1.67.0_1.67.0-13 libboost-system-dev_1.67.0.1+b1 libboost-system1.67-dev_1.67.0-13 libboost-system1.67.0_1.67.0-13 libboost1.67-dev_1.67.0-13 libbsd0_0.9.1-2 libbz2-1.0_1.0.6-9.1 libc-bin_2.28-10+rpi1 libc-dev-bin_2.28-10+rpi1 libc6_2.28-10+rpi1 libc6-dev_2.28-10+rpi1 libcairo-gobject2_1.16.0-4 libcairo-script-interpreter2_1.16.0-4 libcairo2_1.16.0-4 libcairo2-dev_1.16.0-4 libcap-ng0_0.7.9-2 libcc1-0_8.3.0-6+rpi1 libcom-err2_1.44.5-1 libcroco3_0.6.12-3 libdb5.3_5.3.28+dfsg1-0.5 libdebconfclient0_0.249 libdpkg-perl_1.19.7 libeigen3-dev_3.3.7-1 libelf1_0.176-1.1 libexpat1_2.2.6-2 libexpat1-dev_2.2.6-2 libext2fs2_1.44.5-1 libfakeroot_1.23-1 libfdisk1_2.33.1-0.1 libffi-dev_3.2.1-9 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.1.2-1 libfontconfig1_2.13.1-2 libfontconfig1-dev_2.13.1-2 libfreetype6_2.9.1-3 libfreetype6-dev_2.9.1-3 libgcc-8-dev_8.3.0-6+rpi1 libgcc1_1:8.3.0-6+rpi1 libgcrypt20_1.8.4-5 libgdbm-compat4_1.18.1-4 libgdbm6_1.18.1-4 libglib2.0-0_2.58.3-2 libglib2.0-bin_2.58.3-2 libglib2.0-data_2.58.3-2 libglib2.0-dev_2.58.3-2 libglib2.0-dev-bin_2.58.3-2 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.7-4 libgomp1_8.3.0-6+rpi1 libgpg-error0_1.35-1 libhogweed4_3.4.1-1 libice-dev_2:1.0.9-2 libice6_2:1.0.9-2 libicu63_63.2-2 libidn2-0_2.0.5-1 libisl19_0.20-2 libksba8_1.3.5-2 libldap-2.4-2_2.4.47+dfsg-3+rpi1 libldap-common_2.4.47+dfsg-3+rpi1 liblocale-gettext-perl_1.07-3+b3 liblua5.1-0_5.1.5-8.1 liblz4-1_1.8.3-1 liblzma5_5.2.4-1 liblzo2-2_2.10-0.1 libmagic-mgc_1:5.35-4 libmagic1_1:5.35-4 libmount-dev_2.33.1-0.1 libmount1_2.33.1-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncurses6_6.1+20181013-2 libncursesw6_6.1+20181013-2 libnettle6_3.4.1-1 libnpth0_1.6-1 libp11-kit0_0.23.15-2 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre16-3_2:8.39-12 libpcre3_2:8.39-12 libpcre3-dev_2:8.39-12 libpcre32-3_2:8.39-12 libpcrecpp0v5_2:8.39-12 libperl5.28_5.28.1-6 libpipeline1_1.5.1-2 libpixman-1-0_0.36.0-1 libpixman-1-dev_0.36.0-1 libpng-dev_1.6.36-6 libpng16-16_1.6.36-6 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.7.3-1 libpython3.7-minimal_3.7.3-2 libpython3.7-stdlib_3.7.3-2 libreadline7_7.0-5 libsasl2-2_2.1.27+dfsg-1+b1 libsasl2-modules-db_2.1.27+dfsg-1+b1 libseccomp2_2.3.3-4 libselinux1_2.8-1+b1 libselinux1-dev_2.8-1+b1 libsemanage-common_2.8-2 libsemanage1_2.8-2 libsepol1_2.8-1 libsepol1-dev_2.8-1 libsigsegv2_2.12-2 libsm-dev_2:1.2.3-1 libsm6_2:1.2.3-1 libsmartcols1_2.33.1-0.1 libsqlite3-0_3.27.2-3 libss2_1.44.5-1 libssl1.1_1.1.1c-1 libstdc++-8-dev_8.3.0-6+rpi1 libstdc++6_8.3.0-6+rpi1 libsystemd0_241-5+rpi1 libtasn1-6_4.13-3 libtext-charwidth-perl_0.04-7.1+b1 libtext-iconv-perl_1.7-5+b10 libtext-wrapi18n-perl_0.06-7.1 libtinfo5_6.1+20181013-2 libtinfo6_6.1+20181013-2 libtool_2.4.6-9 libubsan1_8.3.0-6+rpi1 libuchardet0_0.0.6-3 libudev1_241-5+rpi1 libunistring2_0.9.10-1 libuuid1_2.33.1-0.1 libx11-6_2:1.6.7-1 libx11-data_2:1.6.7-1 libx11-dev_2:1.6.7-1 libxau-dev_1:1.0.8-1+b2 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-2 libxcb-render0-dev_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb-shm0-dev_1.13.1-2 libxcb1_1.13.1-2 libxcb1-dev_1.13.1-2 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext-dev_2:1.3.3-1+b2 libxext6_2:1.3.3-1+b2 libxml2_2.9.4+dfsg1-7+b1 libxrender-dev_1:0.9.10-1 libxrender1_1:0.9.10-1 libyaml-0-2_0.2.1-1 libzstd1_1.3.8+dfsg-3+rpi1 linux-libc-dev_4.18.20-2+rpi1 login_1:4.5-1.1 lsb-base_10.2019051400+rpi1 m4_1.4.18-2 make_4.2.1-1.2 man-db_2.8.5-2 mawk_1.3.3-17 meson_0.49.2-1 mime-support_3.62 mount_2.33.1-0.1 ncurses-base_6.1+20181013-2 ncurses-bin_6.1+20181013-2 netbase_5.6 ninja-build_1.8.2-1 nlohmann-json3-dev_3.5.0-0.1 pandoc_2.2.1-3+b2 pandoc-data_2.2.1-3 passwd_1:4.5-1.1 patch_2.7.6-3 perl_5.28.1-6 perl-base_5.28.1-6 perl-modules-5.28_5.28.1-6 pinentry-curses_1.1.0-2 pkg-config_0.29-6 po-debconf_1.0.21 python3_3.7.3-1 python3-distutils_3.7.3-1 python3-lib2to3_3.7.3-1 python3-minimal_3.7.3-1 python3-pkg-resources_41.0.1-1 python3.7_3.7.3-2 python3.7-minimal_3.7.3-2 raspbian-archive-keyring_20120528.2 readline-common_7.0-5 sbuild-build-depends-bali-phy-dummy_0.invalid.0 sbuild-build-depends-core-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12 sysvinit-utils_2.93-8 tar_1.30+dfsg-6 tzdata_2019a-1 ucf_3.0038+nmu1 util-linux_2.33.1-0.1 uuid-dev_2.33.1-0.1 x11-common_1:7.7+19 x11proto-core-dev_2018.4-4 x11proto-dev_2018.4-4 x11proto-xext-dev_2018.4-4 xorg-sgml-doctools_1:1.11-1 xtrans-dev_1.3.5-1 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1 zlib1g-dev_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon Jul 8 07:32:17 2019 UTC
gpgv: using RSA key 92978A6E195E4921825F7FF0F34F09744E9F5DD9
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./bali-phy_3.4.1+dfsg-2.dsc
dpkg-source: info: extracting bali-phy in /<<BUILDDIR>>/bali-phy-3.4.1+dfsg
dpkg-source: info: unpacking bali-phy_3.4.1+dfsg.orig.tar.xz
dpkg-source: info: unpacking bali-phy_3.4.1+dfsg-2.debian.tar.xz
Check disk space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=112
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-f130a75c-b13a-4a18-9951-e9edeaa7167f
SCHROOT_UID=107
SCHROOT_USER=buildd
SHELL=/bin/sh
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package bali-phy
dpkg-buildpackage: info: source version 3.4.1+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --buildsystem=meson
dh_auto_clean -O--buildsystem=meson
dh_autoreconf_clean -O--buildsystem=meson
dh_clean -O--buildsystem=meson
debian/rules build-arch
dh build-arch --buildsystem=meson
dh_update_autotools_config -a -O--buildsystem=meson
dh_autoreconf -a -O--buildsystem=meson
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/bali-phy-3.4.1+dfsg'
dh_auto_configure -- -Dextra-tools=false
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 meson .. --wrap-mode=nodownload --buildtype=plain --prefix=/usr --sysconfdir=/etc --localstatedir=/var --libdir=lib/arm-linux-gnueabihf --libexecdir=lib/arm-linux-gnueabihf -Dextra-tools=false
The Meson build system
Version: 0.49.2
Source dir: /<<BUILDDIR>>/bali-phy-3.4.1+dfsg
Build dir: /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf
Build type: native build
Project name: bali-phy
Project version: 3.4.1
Appending CFLAGS from environment: '-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0'
Appending LDFLAGS from environment: '-Wl,-z,relro -Wl,-z,now'
Appending CPPFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2'
Native C compiler: cc (gcc 8.3.0 "cc (Raspbian 8.3.0-6+rpi1) 8.3.0")
Appending CXXFLAGS from environment: '-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0'
Appending LDFLAGS from environment: '-Wl,-z,relro -Wl,-z,now'
Appending CPPFLAGS from environment: '-Wdate-time -D_FORTIFY_SOURCE=2'
Native C++ compiler: c++ (gcc 8.3.0 "c++ (Raspbian 8.3.0-6+rpi1) 8.3.0")
Build machine cpu family: arm
Build machine cpu: armv8l
Has header "sys/resource.h" : YES
Has header "fenv.h" : YES
Checking for function "log2" : YES
Checking for function "feenableexcept" : YES
Configuring config.h using configuration
Compiler for C++ supports arguments -Wno-maybe-uninitialized -Wmaybe-uninitialized: YES
Found pkg-config: /usr/bin/pkg-config (0.29)
Dependency cairo found: YES 1.16.0
Dependency Boost (program_options, random, system, filesystem, chrono) found: YES 1.67
Dependency eigen3 found: YES 3.3.7
Has header "nlohmann/json.hpp" : YES
Library dl found: YES
Program pandoc found: YES (/usr/bin/pandoc)
Program /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/tests/run-tests.py found: YES (/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/tests/run-tests.py)
Build targets in project: 78
Option buildtype is: plain [default: release]
Found ninja-1.8.2 at /usr/bin/ninja
make[1]: Leaving directory '/<<BUILDDIR>>/bali-phy-3.4.1+dfsg'
dh_auto_build -a -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 ninja -j4 -v
[1/256] /usr/bin/meson --internal vcstagger ../src/git-version.h.in src/git-version.h '' /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/src @git_message@ '(.*)' /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/src/git log -n1 '--date=format:%b %d %Y %k:%M:%S' '--pretty=format:[%D commit %h] (%cd)'
[2/256] c++ -Isrc/25a6634@@libsums@sta -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -fno-fast-math -MD -MQ 'src/25a6634@@libsums@sta/computation_machine_sums.cc.o' -MF 'src/25a6634@@libsums@sta/computation_machine_sums.cc.o.d' -o 'src/25a6634@@libsums@sta/computation_machine_sums.cc.o' -c ../src/computation/machine/sums.cc
[3/256] rm -f src/liblibsums.a && gcc-ar csrD src/liblibsums.a 'src/25a6634@@libsums@sta/computation_machine_sums.cc.o'
[4/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/util.cc.o' -MF 'src/25a6634@@bali-phy@sta/util.cc.o.d' -o 'src/25a6634@@bali-phy@sta/util.cc.o' -c ../src/util.cc
[5/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/io.cc.o' -MF 'src/25a6634@@bali-phy@sta/io.cc.o.d' -o 'src/25a6634@@bali-phy@sta/io.cc.o' -c ../src/io.cc
[6/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tree_sequencetree.cc.o' -MF 'src/25a6634@@bali-phy@sta/tree_sequencetree.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tree_sequencetree.cc.o' -c ../src/tree/sequencetree.cc
[7/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/sequence_sequence.cc.o' -MF 'src/25a6634@@bali-phy@sta/sequence_sequence.cc.o.d' -o 'src/25a6634@@bali-phy@sta/sequence_sequence.cc.o' -c ../src/sequence/sequence.cc
[8/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tree_tree-util.cc.o' -MF 'src/25a6634@@bali-phy@sta/tree_tree-util.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tree_tree-util.cc.o' -c ../src/tree/tree-util.cc
[9/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/sequence_alphabet.cc.o' -MF 'src/25a6634@@bali-phy@sta/sequence_alphabet.cc.o.d' -o 'src/25a6634@@bali-phy@sta/sequence_alphabet.cc.o' -c ../src/sequence/alphabet.cc
[10/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tree_tree.cc.o' -MF 'src/25a6634@@bali-phy@sta/tree_tree.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tree_tree.cc.o' -c ../src/tree/tree.cc
[11/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_read-trees.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_read-trees.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_read-trees.cc.o' -c ../src/tools/read-trees.cc
[12/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/sequence_sequence-format.cc.o' -MF 'src/25a6634@@bali-phy@sta/sequence_sequence-format.cc.o.d' -o 'src/25a6634@@bali-phy@sta/sequence_sequence-format.cc.o' -c ../src/sequence/sequence-format.cc
[13/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/rng.cc.o' -MF 'src/25a6634@@bali-phy@sta/rng.cc.o.d' -o 'src/25a6634@@bali-phy@sta/rng.cc.o' -c ../src/rng.cc
../src/rng.cc: In function ‘long unsigned int get_random_seed()’:
../src/rng.cc:42:12: warning: left shift count >= width of type [-Wshift-count-overflow]
s <<= bits_per_read;
^~~~~~~~~~~~~
[14/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_statistics.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_statistics.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_statistics.cc.o' -c ../src/tools/statistics.cc
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from /usr/include/c++/8/valarray:38,
from ../src/tools/statistics.H:24,
from ../src/tools/statistics.cc:22:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from /usr/include/c++/8/valarray:38,
from ../src/tools/statistics.H:24,
from ../src/tools/statistics.cc:22:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘double statistics::quantile(std::vector<double>, double)’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘std::pair<double, double> statistics::central_confidence_interval(std::vector<double>, double)’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘std::pair<double, double> statistics::HPD_confidence_interval(std::vector<double>, double)’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘std::pair<double, double> statistics::mode(std::vector<double>)’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘double statistics::probability_x_less_than_y(const std::valarray<double>&, const std::valarray<double>&)’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[15/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/alignment_alignment-util.cc.o' -MF 'src/25a6634@@bali-phy@sta/alignment_alignment-util.cc.o.d' -o 'src/25a6634@@bali-phy@sta/alignment_alignment-util.cc.o' -c ../src/alignment/alignment-util.cc
[16/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/alignment_load.cc.o' -MF 'src/25a6634@@bali-phy@sta/alignment_load.cc.o.d' -o 'src/25a6634@@bali-phy@sta/alignment_load.cc.o' -c ../src/alignment/load.cc
[17/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/alignment_alignment.cc.o' -MF 'src/25a6634@@bali-phy@sta/alignment_alignment.cc.o.d' -o 'src/25a6634@@bali-phy@sta/alignment_alignment.cc.o' -c ../src/alignment/alignment.cc
[18/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_partition.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_partition.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_partition.cc.o' -c ../src/tools/partition.cc
[19/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/alignment_alignment-random.cc.o' -MF 'src/25a6634@@bali-phy@sta/alignment_alignment-random.cc.o.d' -o 'src/25a6634@@bali-phy@sta/alignment_alignment-random.cc.o' -c ../src/alignment/alignment-random.cc
[20/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tree_randomtree.cc.o' -MF 'src/25a6634@@bali-phy@sta/tree_randomtree.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tree_randomtree.cc.o' -c ../src/tree/randomtree.cc
[21/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/util-random.cc.o' -MF 'src/25a6634@@bali-phy@sta/util-random.cc.o.d' -o 'src/25a6634@@bali-phy@sta/util-random.cc.o' -c ../src/util-random.cc
[22/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_tree-dist.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_tree-dist.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_tree-dist.cc.o' -c ../src/tools/tree-dist.cc
[23/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_parsimony.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_parsimony.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_parsimony.cc.o' -c ../src/tools/parsimony.cc
[24/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/setup.cc.o' -MF 'src/25a6634@@bali-phy@sta/setup.cc.o.d' -o 'src/25a6634@@bali-phy@sta/setup.cc.o' -c ../src/setup.cc
[25/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_findroot.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_findroot.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_findroot.cc.o' -c ../src/tools/findroot.cc
[26/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_stats-table.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_stats-table.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_stats-table.cc.o' -c ../src/tools/stats-table.cc
[27/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_optimize.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_optimize.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_optimize.cc.o' -c ../src/tools/optimize.cc
[28/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_mctree.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_mctree.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_mctree.cc.o' -c ../src/tools/mctree.cc
[29/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/n_indels.cc.o' -MF 'src/25a6634@@bali-phy@sta/n_indels.cc.o.d' -o 'src/25a6634@@bali-phy@sta/n_indels.cc.o' -c ../src/n_indels.cc
[30/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/alignment_index-matrix.cc.o' -MF 'src/25a6634@@bali-phy@sta/alignment_index-matrix.cc.o.d' -o 'src/25a6634@@bali-phy@sta/alignment_index-matrix.cc.o' -c ../src/alignment/index-matrix.cc
[31/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_distance-report.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_distance-report.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_distance-report.cc.o' -c ../src/tools/distance-report.cc
[32/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_inverse.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_inverse.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_inverse.cc.o' -c ../src/tools/inverse.cc
[33/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_distance-methods.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_distance-methods.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_distance-methods.cc.o' -c ../src/tools/distance-methods.cc
[34/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_joint-A-T.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_joint-A-T.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_joint-A-T.cc.o' -c ../src/tools/joint-A-T.cc
[35/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_dp_hmm.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_dp_hmm.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_dp_hmm.cc.o' -c ../src/dp/dp_hmm.cc
[36/256] c++ -Isrc/25a6634@@bali-phy@sta -Isrc -I../src -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/25a6634@@bali-phy@sta/tools_consensus-tree.cc.o' -MF 'src/25a6634@@bali-phy@sta/tools_consensus-tree.cc.o.d' -o 'src/25a6634@@bali-phy@sta/tools_consensus-tree.cc.o' -c ../src/tools/consensus-tree.cc
[37/256] rm -f src/libbali-phy.a && gcc-ar csrD src/libbali-phy.a 'src/25a6634@@bali-phy@sta/io.cc.o' 'src/25a6634@@bali-phy@sta/util.cc.o' 'src/25a6634@@bali-phy@sta/tree_sequencetree.cc.o' 'src/25a6634@@bali-phy@sta/tree_tree.cc.o' 'src/25a6634@@bali-phy@sta/sequence_alphabet.cc.o' 'src/25a6634@@bali-phy@sta/sequence_sequence.cc.o' 'src/25a6634@@bali-phy@sta/tree_tree-util.cc.o' 'src/25a6634@@bali-phy@sta/tools_read-trees.cc.o' 'src/25a6634@@bali-phy@sta/sequence_sequence-format.cc.o' 'src/25a6634@@bali-phy@sta/alignment_alignment-util.cc.o' 'src/25a6634@@bali-phy@sta/rng.cc.o' 'src/25a6634@@bali-phy@sta/alignment_load.cc.o' 'src/25a6634@@bali-phy@sta/alignment_alignment.cc.o' 'src/25a6634@@bali-phy@sta/tools_statistics.cc.o' 'src/25a6634@@bali-phy@sta/tools_partition.cc.o' 'src/25a6634@@bali-phy@sta/tools_tree-dist.cc.o' 'src/25a6634@@bali-phy@sta/alignment_alignment-random.cc.o' 'src/25a6634@@bali-phy@sta/setup.cc.o' 'src/25a6634@@bali-phy@sta/tree_randomtree.cc.o' 'src/25a6634@@bali-phy@sta/util-random.cc.o' 'src/25a6634@@bali-phy@sta/tools_parsimony.cc.o' 'src/25a6634@@bali-phy@sta/alignment_index-matrix.cc.o' 'src/25a6634@@bali-phy@sta/tools_mctree.cc.o' 'src/25a6634@@bali-phy@sta/tools_stats-table.cc.o' 'src/25a6634@@bali-phy@sta/tools_findroot.cc.o' 'src/25a6634@@bali-phy@sta/tools_optimize.cc.o' 'src/25a6634@@bali-phy@sta/tools_distance-report.cc.o' 'src/25a6634@@bali-phy@sta/n_indels.cc.o' 'src/25a6634@@bali-phy@sta/tools_inverse.cc.o' 'src/25a6634@@bali-phy@sta/tools_joint-A-T.cc.o' 'src/25a6634@@bali-phy@sta/tools_distance-methods.cc.o' 'src/25a6634@@bali-phy@sta/tools_consensus-tree.cc.o'
[38/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/parser_driver.cc.o' -MF 'src/25a6634@@bali-phy@exe/parser_driver.cc.o.d' -o 'src/25a6634@@bali-phy@exe/parser_driver.cc.o' -c ../src/parser/driver.cc
[39/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/parser_rename.cc.o' -MF 'src/25a6634@@bali-phy@exe/parser_rename.cc.o.d' -o 'src/25a6634@@bali-phy@exe/parser_rename.cc.o' -c ../src/parser/rename.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/parser/rename.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/deque:66,
from ../src/parser/rename.cc:5:
/usr/include/c++/8/bits/deque.tcc: In member function ‘void std::deque<_Tp, _Alloc>::_M_insert_aux(std::deque<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::deque<_Tp, _Alloc>::size_type) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const expression_ref*, std::vector<expression_ref> >; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/deque.tcc:758:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
deque<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/deque.tcc:758:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from ../src/parser/rename.cc:2:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘bound_var_info renamer_state::rename_pattern(expression_ref&, bool)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[40/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/parser_desugar.cc.o' -MF 'src/25a6634@@bali-phy@exe/parser_desugar.cc.o.d' -o 'src/25a6634@@bali-phy@exe/parser_desugar.cc.o' -c ../src/parser/desugar.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/parser/desugar.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/parser/desugar.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/parser/desugar.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘std::vector<expression_ref> desugar_state::parse_fundecls(const std::vector<expression_ref>&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/parser/desugar.cc:1:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/parser/desugar.cc:1:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/parser/desugar.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘expression_ref desugar_state::desugar(const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
/usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/parser/desugar.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘CDecls desugar_state::desugar_decls(const expression_ref&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[41/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/parser_desugar-case.cc.o' -MF 'src/25a6634@@bali-phy@exe/parser_desugar-case.cc.o.d' -o 'src/25a6634@@bali-phy@exe/parser_desugar-case.cc.o' -c ../src/parser/desugar-case.cc
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/parser/desugar-case.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type ‘std::initializer_list<std::pair<var, expression_ref> >’ changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/parser/desugar-case.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In static member function ‘static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = expression_ref; _Functor = desugar_state::match_constant(const std::vector<expression_ref>&, const std::vector<equation_info_t>&)::<lambda(const expression_ref&)>; _ArgTypes = {const expression_ref&}]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<const expression_ref*, std::vector<expression_ref> >; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/parser/desugar-case.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘failable_expression desugar_state::match_constant(const std::vector<expression_ref>&, const std::vector<equation_info_t>&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
^~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
_M_range_insert(__pos, __first, __last,
^~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<const expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/parser/desugar-case.cc:1:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/parser/desugar-case.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘failable_expression desugar_state::match_var(const std::vector<expression_ref>&, const std::vector<equation_info_t>&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
../src/parser/desugar-case.cc: In member function ‘void desugar_state::clean_up_pattern(const expression_ref&, equation_info_t&)’:
../src/parser/desugar-case.cc:310:17: note: parameter passing for argument of type ‘std::initializer_list<std::pair<var, expression_ref> >’ changed in GCC 7.1
rhs.add_binding({{y, x}});
~~~~~~~~~~~~~~~^~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/parser/desugar-case.cc:1:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
../src/parser/desugar-case.cc:330:17: note: parameter passing for argument of type ‘std::initializer_list<std::pair<var, expression_ref> >’ changed in GCC 7.1
rhs.add_binding({{y, x}});
~~~~~~~~~~~~~~~^~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/parser/desugar-case.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘expression_ref desugar_state::def_function(const std::vector<equation_info_t>&, const expression_ref&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[42/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/parser_lexer.cc.o' -MF 'src/25a6634@@bali-phy@exe/parser_lexer.cc.o.d' -o 'src/25a6634@@bali-phy@exe/parser_lexer.cc.o' -c ../src/parser/lexer.cc
[43/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/util_ptree.cc.o' -MF 'src/25a6634@@bali-phy@exe/util_ptree.cc.o.d' -o 'src/25a6634@@bali-phy@exe/util_ptree.cc.o' -c ../src/util/ptree.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/util/ptree.H:5,
from ../src/util/ptree.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util/ptree.H:5,
from ../src/util/ptree.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘void to_json(nlohmann::json&, const ptree&)’:
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[44/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/substitution_substitution.cc.o' -MF 'src/25a6634@@bali-phy@exe/substitution_substitution.cc.o.d' -o 'src/25a6634@@bali-phy@exe/substitution_substitution.cc.o' -c ../src/substitution/substitution.cc
[45/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/math_exponential.cc.o' -MF 'src/25a6634@@bali-phy@exe/math_exponential.cc.o.d' -o 'src/25a6634@@bali-phy@exe/math_exponential.cc.o' -c ../src/math/exponential.cc
[46/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_moves.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_moves.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_moves.cc.o' -c ../src/mcmc/moves.cc
[47/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/parser_parser.cc.o' -MF 'src/25a6634@@bali-phy@exe/parser_parser.cc.o.d' -o 'src/25a6634@@bali-phy@exe/parser_parser.cc.o' -c ../src/parser/parser.cc
In file included from /usr/include/c++/8/vector:64,
from parser.y:14,
from parser.cc:46:
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/stl_vector.h:515:7: note: parameter passing for argument of type ‘std::initializer_list<expression_ref>’ changed in GCC 7.1
vector(initializer_list<value_type> __l,
^~~~~~
In file included from /usr/include/c++/8/vector:69,
from parser.y:14,
from parser.cc:46:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from parser.y:14,
from parser.cc:46:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from parser.y:14,
from parser.cc:46:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {yy::parser::stack_symbol_type}; _Tp = yy::parser::stack_symbol_type; _Alloc = std::allocator<yy::parser::stack_symbol_type>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<yy::parser::stack_symbol_type, std::allocator<yy::parser::stack_symbol_type> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<yy::parser::stack_symbol_type*, std::vector<yy::parser::stack_symbol_type, std::allocator<yy::parser::stack_symbol_type> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void yy::stack<T, S>::push(T&) [with T = yy::parser::stack_symbol_type; S = std::vector<yy::parser::stack_symbol_type, std::allocator<yy::parser::stack_symbol_type> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<yy::parser::stack_symbol_type*, std::vector<yy::parser::stack_symbol_type, std::allocator<yy::parser::stack_symbol_type> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void yy::parser::yypush_(const char*, yy::parser::stack_symbol_type&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<yy::parser::stack_symbol_type*, std::vector<yy::parser::stack_symbol_type, std::allocator<yy::parser::stack_symbol_type> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref yy_make_string(const string&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from parser.y:14,
from parser.cc:46:
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref yy_make_alt(const expression_ref&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref make_lambda(const std::vector<expression_ref>&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from parser.y:14,
from parser.cc:46:
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref make_infix(const string&, boost::optional<int>&, std::vector<std::__cxx11::basic_string<char> >&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
parser.y: In member function ‘virtual int yy::parser::parse()’:
parser.y:887:55: note: parameter passing for argument of type ‘std::initializer_list<expression_ref>’ changed in GCC 7.1
parser.y:976:55: note: parameter passing for argument of type ‘std::initializer_list<expression_ref>’ changed in GCC 7.1
parser.y:1131:45: note: parameter passing for argument of type ‘std::initializer_list<expression_ref>’ changed in GCC 7.1
parser.y:1132:45: note: parameter passing for argument of type ‘std::initializer_list<expression_ref>’ changed in GCC 7.1
parser.y:1133:45: note: parameter passing for argument of type ‘std::initializer_list<expression_ref>’ changed in GCC 7.1
parser.y:1134:45: note: parameter passing for argument of type ‘std::initializer_list<expression_ref>’ changed in GCC 7.1
[48/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/prior.cc.o' -MF 'src/25a6634@@bali-phy@exe/prior.cc.o.d' -o 'src/25a6634@@bali-phy@exe/prior.cc.o' -c ../src/prior.cc
[49/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/math_eigenvalue.cc.o' -MF 'src/25a6634@@bali-phy@exe/math_eigenvalue.cc.o.d' -o 'src/25a6634@@bali-phy@exe/math_eigenvalue.cc.o' -c ../src/math/eigenvalue.cc
[50/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/probability_choose.cc.o' -MF 'src/25a6634@@bali-phy@exe/probability_choose.cc.o.d' -o 'src/25a6634@@bali-phy@exe/probability_choose.cc.o' -c ../src/probability/choose.cc
[51/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_mcmc.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_mcmc.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_mcmc.cc.o' -c ../src/mcmc/mcmc.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/mcmc/mcmc.H:35,
from ../src/mcmc/mcmc.cc:34:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: 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
In file included from /usr/include/c++/8/vector:64,
from ../src/mcmc/mcmc.H:35,
from ../src/mcmc/mcmc.cc:34:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void MCMC::MoveGroupBase::add(double, const MCMC::Move&, bool)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[52/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_sample-branch-lengths.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_sample-branch-lengths.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_sample-branch-lengths.cc.o' -c ../src/mcmc/sample-branch-lengths.cc
[53/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/util_text.cc.o' -MF 'src/25a6634@@bali-phy@exe/util_text.cc.o.d' -o 'src/25a6634@@bali-phy@exe/util_text.cc.o' -c ../src/util/text.cc
[54/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/models_parameters.cc.o' -MF 'src/25a6634@@bali-phy@exe/models_parameters.cc.o.d' -o 'src/25a6634@@bali-phy@exe/models_parameters.cc.o' -c ../src/models/parameters.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/sequence/alphabet.H:27,
from ../src/models/parameters.H:34,
from ../src/models/parameters.cc:31:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/sequence/alphabet.H:27,
from ../src/models/parameters.H:34,
from ../src/models/parameters.cc:31:
/usr/include/c++/8/bits/stl_vector.h: In constructor ‘data_partition_constants::data_partition_constants(Parameters*, int, const alignment&, const std::vector<int>&, int)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[55/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_dp-engine.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_dp-engine.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_dp-engine.cc.o' -c ../src/dp/dp-engine.cc
[56/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/models_TreeInterface.cc.o' -MF 'src/25a6634@@bali-phy@exe/models_TreeInterface.cc.o.d' -o 'src/25a6634@@bali-phy@exe/models_TreeInterface.cc.o' -c ../src/models/TreeInterface.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/tree/tree.H:31,
from ../src/models/TreeInterface.cc:1:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘std::__cxx11::string write(const TreeInterface&, const std::vector<std::__cxx11::basic_string<char> >&, bool)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[57/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_hmm.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_hmm.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_hmm.cc.o' -c ../src/dp/hmm.cc
[58/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/bali-phy.cc.o' -MF 'src/25a6634@@bali-phy@exe/bali-phy.cc.o.d' -o 'src/25a6634@@bali-phy@exe/bali-phy.cc.o' -c ../src/bali-phy.cc
[59/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_dp-array.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_dp-array.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_dp-array.cc.o' -c ../src/dp/dp-array.cc
[60/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_3way.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_3way.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_3way.cc.o' -c ../src/dp/3way.cc
[61/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_dp-matrix.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_dp-matrix.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_dp-matrix.cc.o' -c ../src/dp/dp-matrix.cc
[62/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_sample-alignment.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_sample-alignment.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_sample-alignment.cc.o' -c ../src/mcmc/sample-alignment.cc
[63/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_2way.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_2way.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_2way.cc.o' -c ../src/dp/2way.cc
[64/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/imodel_imodel.cc.o' -MF 'src/25a6634@@bali-phy@exe/imodel_imodel.cc.o.d' -o 'src/25a6634@@bali-phy@exe/imodel_imodel.cc.o' -c ../src/imodel/imodel.cc
[65/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_sample-node.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_sample-node.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_sample-node.cc.o' -c ../src/mcmc/sample-node.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/tree/tree.H:31,
from ../src/mcmc/sample.H:23,
from ../src/mcmc/sample-node.cc:28:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {log_double_t}; _Tp = log_double_t; _Alloc = std::allocator<log_double_t>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<log_double_t>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘int sample_node_multi(std::vector<Parameters>&, const std::vector<std::vector<int> >&, const std::vector<log_double_t>&, bool, bool)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[66/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_5way.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_5way.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_5way.cc.o' -c ../src/dp/5way.cc
[67/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_sample-topology-NNI.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_sample-topology-NNI.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_sample-topology-NNI.cc.o' -c ../src/mcmc/sample-topology-NNI.cc
[68/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_dp-cube.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_dp-cube.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_dp-cube.cc.o' -c ../src/dp/dp-cube.cc
[69/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_sample-two-nodes.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_sample-two-nodes.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_sample-two-nodes.cc.o' -c ../src/mcmc/sample-two-nodes.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/tree/tree.H:31,
from ../src/mcmc/sample.H:23,
from ../src/mcmc/sample-two-nodes.cc:29:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {log_double_t}; _Tp = log_double_t; _Alloc = std::allocator<log_double_t>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<log_double_t>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘int sample_two_nodes_multi(std::vector<Parameters>&, const std::vector<A5::hmm_order>&, const std::vector<log_double_t>&, bool, bool)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[70/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_sample-cube.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_sample-cube.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_sample-cube.cc.o' -c ../src/mcmc/sample-cube.cc
[71/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/dp_alignment-sums.cc.o' -MF 'src/25a6634@@bali-phy@exe/dp_alignment-sums.cc.o.d' -o 'src/25a6634@@bali-phy@exe/dp_alignment-sums.cc.o' -c ../src/dp/alignment-sums.cc
[72/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/models_setup.cc.o' -MF 'src/25a6634@@bali-phy@exe/models_setup.cc.o.d' -o 'src/25a6634@@bali-phy@exe/models_setup.cc.o' -c ../src/models/setup.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/models/setup.cc:79:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {pretty_model_t}; _Tp = pretty_model_t; _Alloc = std::allocator<pretty_model_t>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<pretty_model_t>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<pretty_model_t*, std::vector<pretty_model_t> >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > extract_terms(ptree&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In constructor ‘pretty_model_t::pretty_model_t(const ptree&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<pretty_model_t*, std::vector<pretty_model_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/models/setup.cc:79:
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::pair<expression_ref, std::set<std::__cxx11::basic_string<char> > > get_model_function(const Rules&, const ptree&, const names_in_scope_t&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/models/setup.cc:79:
/usr/include/c++/8/bits/vector.tcc: In function ‘model_t get_model(const Rules&, const string&, const string&, const std::vector<std::pair<std::__cxx11::basic_string<char>, std::__cxx11::basic_string<char> > >&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/models/setup.cc:79:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::value_type& nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::operator[](nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::size_type) [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’:
/usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_fill_insert(begin() + __offset, __n, __x);
^~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘void to_json(nlohmann::json&, const pretty_model_t&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[73/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_sample-topology-SPR.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_sample-topology-SPR.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_sample-topology-SPR.cc.o' -c ../src/mcmc/sample-topology-SPR.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/tree/tree.H:31,
from ../src/mcmc/sample.H:23,
from ../src/mcmc/sample-topology-SPR.cc:30:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const log_double_t&}; _Tp = log_double_t; _Alloc = std::allocator<log_double_t>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<log_double_t>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/tree/tree.H:31,
from ../src/mcmc/sample.H:23,
from ../src/mcmc/sample-topology-SPR.cc:30:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘std::vector<T> spr_info::convert_to_vector(const std::map<tree_edge, U>&) const [with U = log_double_t]’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[74/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/startup_help.cc.o' -MF 'src/25a6634@@bali-phy@exe/startup_help.cc.o.d' -o 'src/25a6634@@bali-phy@exe/startup_help.cc.o' -c ../src/startup/help.cc
[75/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/probability_probability.cc.o' -MF 'src/25a6634@@bali-phy@exe/probability_probability.cc.o.d' -o 'src/25a6634@@bali-phy@exe/probability_probability.cc.o' -c ../src/probability/probability.cc
[76/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/myexception.cc.o' -MF 'src/25a6634@@bali-phy@exe/myexception.cc.o.d' -o 'src/25a6634@@bali-phy@exe/myexception.cc.o' -c ../src/myexception.cc
[77/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/math_pow2.cc.o' -MF 'src/25a6634@@bali-phy@exe/math_pow2.cc.o.d' -o 'src/25a6634@@bali-phy@exe/math_pow2.cc.o' -c ../src/math/pow2.cc
[78/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/alignment_alignment-constraint.cc.o' -MF 'src/25a6634@@bali-phy@exe/alignment_alignment-constraint.cc.o.d' -o 'src/25a6634@@bali-phy@exe/alignment_alignment-constraint.cc.o' -c ../src/alignment/alignment-constraint.cc
[79/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/monitor.cc.o' -MF 'src/25a6634@@bali-phy@exe/monitor.cc.o.d' -o 'src/25a6634@@bali-phy@exe/monitor.cc.o' -c ../src/monitor.cc
../src/monitor.cc: In function ‘void report_mem()’:
../src/monitor.cc:113:9: warning: ignoring return value of ‘int system(const char*)’, declared with attribute warn_unused_result [-Wunused-result]
system(cmd.str().c_str());
~~~~~~^~~~~~~~~~~~~~~~~~~
[80/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/models_model.cc.o' -MF 'src/25a6634@@bali-phy@exe/models_model.cc.o.d' -o 'src/25a6634@@bali-phy@exe/models_model.cc.o' -c ../src/models/model.cc
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/detail/container_fwd.hpp:93,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from ../src/models/model.cc:23:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘std::vector<expression_ref> model_parameter_expressions(const Model&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘void simplify(ptree&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/set:60,
from ../src/models/model.cc:20:
/usr/include/c++/8/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>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/detail/container_fwd.hpp:93,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from ../src/models/model.cc:23:
/usr/include/c++/8/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from /usr/include/boost/detail/container_fwd.hpp:93,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from ../src/models/model.cc:23:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘IteratorType nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::erase(IteratorType) [with IteratorType = nlohmann::detail::iter_impl<nlohmann::basic_json<> >; typename std::enable_if<(std::is_same<InputIT, nlohmann::detail::iter_impl<nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > >::value || std::is_same<InputIT, nlohmann::detail::iter_impl<const nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > >::value), int>::type <anonymous> = 0; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’:
/usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/detail/container_fwd.hpp:93,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from ../src/models/model.cc:23:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::start_array(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::start_object(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {bool&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘BasicJsonType* nlohmann::detail::json_sax_dom_parser<BasicJsonType>::handle_value(Value&&) [with Value = bool&; BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/set:60,
from ../src/models/model.cc:20:
/usr/include/c++/8/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>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<void>; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../src/models/model.cc:21:
/usr/include/c++/8/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 = std::__cxx11::basic_string<char>; _Tp = nlohmann::basic_json<>; _Compare = std::less<void>; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/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>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function ‘bool nlohmann::detail::json_sax_dom_callback_parser<BasicJsonType>::key(nlohmann::detail::json_sax_dom_callback_parser<BasicJsonType>::string_t&) [with BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/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>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/detail/container_fwd.hpp:93,
from /usr/include/boost/container_hash/extensions.hpp:22,
from /usr/include/boost/container_hash/hash.hpp:760,
from /usr/include/boost/type_index/stl_type_index.hpp:43,
from /usr/include/boost/type_index.hpp:29,
from /usr/include/boost/variant/variant.hpp:21,
from /usr/include/boost/variant.hpp:17,
from ../src/models/model.cc:23:
/usr/include/c++/8/bits/vector.tcc: In member function ‘bool nlohmann::detail::parser<BasicJsonType>::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser<nlohmann::basic_json<> >; BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../src/models/model.cc:21:
/usr/include/c++/8/bits/stl_map.h: In function ‘Model::key_map_t parse_key_map(const std::vector<std::__cxx11::basic_string<char> >&)’:
/usr/include/c++/8/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>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
[81/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/substitution_parsimony.cc.o' -MF 'src/25a6634@@bali-phy@exe/substitution_parsimony.cc.o.d' -o 'src/25a6634@@bali-phy@exe/substitution_parsimony.cc.o' -c ../src/substitution/parsimony.cc
[82/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/n_indels2.cc.o' -MF 'src/25a6634@@bali-phy@exe/n_indels2.cc.o.d' -o 'src/25a6634@@bali-phy@exe/n_indels2.cc.o' -c ../src/n_indels2.cc
[83/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/alignment_alignment-util2.cc.o' -MF 'src/25a6634@@bali-phy@exe/alignment_alignment-util2.cc.o.d' -o 'src/25a6634@@bali-phy@exe/alignment_alignment-util2.cc.o' -c ../src/alignment/alignment-util2.cc
[84/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/version.cc.o' -MF 'src/25a6634@@bali-phy@exe/version.cc.o.d' -o 'src/25a6634@@bali-phy@exe/version.cc.o' -c ../src/version.cc
../src/version.cc:67:8: warning: macro "__DATE__" might prevent reproducible builds [-Wdate-time]
s<<__DATE__<<" "<<__TIME__;
^~~~~~~~
../src/version.cc:67:23: warning: macro "__TIME__" might prevent reproducible builds [-Wdate-time]
s<<__DATE__<<" "<<__TIME__;
^~~~~~~~
[85/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/tools_parsimony2.cc.o' -MF 'src/25a6634@@bali-phy@exe/tools_parsimony2.cc.o.d' -o 'src/25a6634@@bali-phy@exe/tools_parsimony2.cc.o' -c ../src/tools/parsimony2.cc
[86/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/timer_stack.cc.o' -MF 'src/25a6634@@bali-phy@exe/timer_stack.cc.o.d' -o 'src/25a6634@@bali-phy@exe/timer_stack.cc.o' -c ../src/timer_stack.cc
[87/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_proposals.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_proposals.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_proposals.cc.o' -c ../src/mcmc/proposals.cc
[88/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_slice-sampling.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_slice-sampling.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_slice-sampling.cc.o' -c ../src/mcmc/slice-sampling.cc
[89/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_operator.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_operator.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_operator.cc.o' -c ../src/computation/expression/operator.cc
[90/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_AIS.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_AIS.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_AIS.cc.o' -c ../src/mcmc/AIS.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/mcmc/mcmc.H:35,
from ../src/mcmc/AIS.H:4,
from ../src/mcmc/AIS.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const log_double_t&}; _Tp = log_double_t; _Alloc = std::allocator<log_double_t>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<log_double_t>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/mcmc/mcmc.H:35,
from ../src/mcmc/AIS.H:4,
from ../src/mcmc/AIS.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void AIS_Sampler::go(owned_ptr<Model>&, std::ostream&, std::vector<double>)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[91/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_constructor.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_constructor.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_constructor.cc.o' -c ../src/computation/expression/constructor.cc
[92/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_logger.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_logger.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_logger.cc.o' -c ../src/mcmc/logger.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/mcmc/mcmc.H:35,
from ../src/mcmc/logger.cc:33:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const log_double_t&}; _Tp = log_double_t; _Alloc = std::allocator<log_double_t>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<log_double_t>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/mcmc/mcmc.H:35,
from ../src/mcmc/logger.cc:33:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘std::__cxx11::string MCMC::Get_Rao_Blackwellized_Parameter_Function::operator()(const Model&, long int)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<log_double_t*, std::vector<log_double_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[93/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_expression.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_expression.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_expression.cc.o' -c ../src/computation/expression/expression.cc
[94/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_AST_node.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_AST_node.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_AST_node.cc.o' -c ../src/computation/expression/AST_node.cc
[95/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_setup.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_setup.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_setup.cc.o' -c ../src/mcmc/setup.cc
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/program_options/errors.hpp:14,
from /usr/include/boost/program_options/options_description.hpp:12,
from /usr/include/boost/program_options.hpp:15,
from ../src/mcmc/setup.H:34,
from ../src/mcmc/setup.cc:31:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from /usr/include/boost/program_options/errors.hpp:15,
from /usr/include/boost/program_options/options_description.hpp:12,
from /usr/include/boost/program_options.hpp:15,
from ../src/mcmc/setup.H:34,
from ../src/mcmc/setup.cc:31:
/usr/include/c++/8/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>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from /usr/include/boost/program_options/errors.hpp:15,
from /usr/include/boost/program_options/options_description.hpp:12,
from /usr/include/boost/program_options.hpp:15,
from ../src/mcmc/setup.H:34,
from ../src/mcmc/setup.cc:31:
/usr/include/c++/8/bits/stl_map.h: In function ‘void add_MH_move(Model&, const proposal_fn&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<std::__cxx11::basic_string<char> >&, const std::vector<double>&, MCMC::MoveAll&, double)’:
/usr/include/c++/8/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>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/program_options/errors.hpp:14,
from /usr/include/boost/program_options/options_description.hpp:12,
from /usr/include/boost/program_options.hpp:15,
from ../src/mcmc/setup.H:34,
from ../src/mcmc/setup.cc:31:
/usr/include/c++/8/bits/vector.tcc: In function ‘void do_sampling(const boost::program_options::variables_map&, owned_ptr<Model>&, long int, std::ostream&, const std::vector<std::function<void(const Model&, long int)> >&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[96/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_apply.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_apply.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_apply.cc.o' -c ../src/computation/expression/apply.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/expression/expression_ref.H:4,
from ../src/computation/expression/apply.H:4,
from ../src/computation/expression/apply.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/expression/expression_ref.H:4,
from ../src/computation/expression/apply.H:4,
from ../src/computation/expression/apply.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref apply_expression(const expression_ref&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[97/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_expression_ref.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_expression_ref.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_expression_ref.cc.o' -c ../src/computation/expression/expression_ref.cc
../src/computation/expression/expression_ref.cc: In constructor ‘expression::expression(const expression_ref&, std::initializer_list<expression_ref>)’:
../src/computation/expression/expression_ref.cc:240:1: note: parameter passing for argument of type ‘const std::initializer_list<expression_ref>’ changed in GCC 7.1
expression::expression(const expression_ref& H, const std::initializer_list< expression_ref > S)
^~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/computation/expression/expression_ref.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util.H:31,
from ../src/computation/expression/expression_ref.cc:3:
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::unique_ptr<expression> operator+(const expression_ref&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::unique_ptr<expression> operator+(const expression&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[98/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_substitute.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_substitute.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_substitute.cc.o' -c ../src/computation/expression/substitute.cc
[99/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_indexify.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_indexify.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_indexify.cc.o' -c ../src/computation/expression/indexify.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/expression/indexify.H:4,
from ../src/computation/expression/indexify.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref indexify(const expression_ref&, std::vector<var>&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref deindexify(const expression_ref&, const std::vector<expression_ref>&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[100/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_case.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_case.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_case.cc.o' -c ../src/computation/expression/case.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/lambda.H:4,
from ../src/computation/expression/case.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/lambda.H:4,
from ../src/computation/expression/case.cc:2:
/usr/include/c++/8/bits/stl_vector.h: In function ‘bool parse_case_expression(const expression_ref&, expression_ref&, std::vector<expression_ref>&, std::vector<expression_ref>&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref make_case_expression(const expression_ref&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/lambda.H:4,
from ../src/computation/expression/case.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/lambda.H:4,
from ../src/computation/expression/case.cc:2:
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref make_alt(const expression_ref&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/lambda.H:4,
from ../src/computation/expression/case.cc:2:
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref make_alts(const std::vector<expression_ref>&, const std::vector<expression_ref>&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[101/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_tuple.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_tuple.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_tuple.cc.o' -c ../src/computation/expression/tuple.cc
[102/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_let.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_let.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_let.cc.o' -c ../src/computation/expression/let.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref indexed_let_expression(const std::vector<expression_ref>&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function ‘void get_decls(const expression_ref&, CDecls&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref make_decls(const CDecls&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref let_expression(const CDecls&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref make_topdecls(const CDecls&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/var.H:4,
from ../src/computation/expression/let.cc:1:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[103/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_trim.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_trim.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_trim.cc.o' -c ../src/computation/expression/trim.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/trim.H:4,
from ../src/computation/expression/trim.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref make_trim(const expression_ref&, const std::vector<int>&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/trim.H:4,
from ../src/computation/expression/trim.cc:1:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/trim.H:4,
from ../src/computation/expression/trim.cc:1:
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref remap_free_indices(const expression_ref&, const std::vector<int>&, int)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[104/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_list.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_list.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_list.cc.o' -c ../src/computation/expression/list.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/expression/list.H:4,
from ../src/computation/expression/list.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/expression/list.H:4,
from ../src/computation/expression/list.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref cons(const expression_ref&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::vector<expression_ref> get_ref_vector_from_list(const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/expression/list.H:4,
from ../src/computation/expression/list.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref char_list(const string&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[105/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_lambda.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_lambda.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_lambda.cc.o' -c ../src/computation/expression/lambda.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/expression/lambda.H:4,
from ../src/computation/expression/lambda.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref lambda_expression(const Operator&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[106/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_var.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_var.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_var.cc.o' -c ../src/computation/expression/var.cc
[107/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_machine_args.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_machine_args.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_machine_args.cc.o' -c ../src/computation/machine/args.cc
[108/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_machine_tokens.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_machine_tokens.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_machine_tokens.cc.o' -c ../src/computation/machine/tokens.cc
[109/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_preprocess.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_preprocess.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_preprocess.cc.o' -c ../src/computation/preprocess.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/machine/graph_register.H:5,
from ../src/computation/preprocess.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref graph_normalize(const expression_ref&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[110/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_machine_graph_register.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_machine_graph_register.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_machine_graph_register.cc.o' -c ../src/computation/machine/graph_register.cc
[111/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_machine_show_graph.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_machine_show_graph.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_machine_show_graph.cc.o' -c ../src/computation/machine/show_graph.cc
In file included from /usr/include/c++/8/map:60,
from ../src/util.H:37,
from ../src/object.H:7,
from ../src/computation/machine/graph_register.H:7,
from ../src/computation/machine/show_graph.cc:2:
/usr/include/c++/8/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 int&>, std::tuple<>}; _Key = int; _Val = std::pair<const int, expression_ref>; _KeyOfValue = std::_Select1st<std::pair<const int, expression_ref> >; _Compare = std::less<int>; _Alloc = std::allocator<std::pair<const int, expression_ref> >]’:
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, expression_ref>, std::_Select1st<std::pair<const int, expression_ref> >, std::less<int>, std::allocator<std::pair<const int, expression_ref> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const int, expression_ref> >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../src/util.H:37,
from ../src/object.H:7,
from ../src/computation/machine/graph_register.H:7,
from ../src/computation/machine/show_graph.cc:2:
/usr/include/c++/8/bits/stl_map.h: In function ‘void discover_graph_vars(const reg_heap&, int, std::map<int, expression_ref>&, const std::map<std::__cxx11::basic_string<char>, int>&)’:
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, expression_ref>, std::_Select1st<std::pair<const int, expression_ref> >, std::less<int>, std::allocator<std::pair<const int, expression_ref> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const int, expression_ref> >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, expression_ref>, std::_Select1st<std::pair<const int, expression_ref> >, std::less<int>, std::allocator<std::pair<const int, expression_ref> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const int, expression_ref> >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, expression_ref>, std::_Select1st<std::pair<const int, expression_ref> >, std::less<int>, std::allocator<std::pair<const int, expression_ref> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const int, expression_ref> >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, expression_ref>, std::_Select1st<std::pair<const int, expression_ref> >, std::less<int>, std::allocator<std::pair<const int, expression_ref> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const int, expression_ref> >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree<int, std::pair<const int, expression_ref>, std::_Select1st<std::pair<const int, expression_ref> >, std::less<int>, std::allocator<std::pair<const int, expression_ref> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const int, expression_ref> >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
[112/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_machine_evaluate.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_machine_evaluate.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_machine_evaluate.cc.o' -c ../src/computation/machine/evaluate.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/machine/graph_register.H:5,
from ../src/computation/machine/evaluate.cc:5:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const closure&}; _Tp = closure; _Alloc = std::allocator<closure>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<closure>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<closure*, std::vector<closure> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/machine/graph_register.H:5,
from ../src/computation/machine/evaluate.cc:5:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void reg_heap::incremental_evaluate_from_call(int, closure&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<closure*, std::vector<closure> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function ‘std::pair<int, int> reg_heap::incremental_evaluate_(int)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<closure*, std::vector<closure> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<closure*, std::vector<closure> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[113/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_machine_gc.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_machine_gc.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_machine_gc.cc.o' -c ../src/computation/machine/gc.cc
[114/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_module.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_module.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_module.cc.o' -c ../src/computation/module.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::vector<expression_ref> peel_lambdas(expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘void parse_combinator_application(const expression_ref&, std::__cxx11::string&, std::vector<expression_ref>&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref func_type(const expression_ref&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/set:60,
from ../src/computation/module.cc:1:
/usr/include/c++/8/bits/stl_tree.h: In member function ‘void std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_insert_unique(_II, _II) [with _InputIterator = std::_Rb_tree_const_iterator<std::pair<const var, expression_ref> >; _Key = var; _Val = std::pair<const var, expression_ref>; _KeyOfValue = std::_Select1st<std::pair<const var, expression_ref> >; _Compare = std::less<var>; _Alloc = std::allocator<std::pair<const var, expression_ref> >]’:
/usr/include/c++/8/bits/stl_tree.h:2463:7: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<std::pair<const var, expression_ref> >’ changed in GCC 7.1
_Rb_tree<_Key, _Val, _KoV, _Cmp, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_tree.h:2463:7: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<std::pair<const var, expression_ref> >’ changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref rename_top_level(const expression_ref&, const string&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/set:60,
from ../src/computation/module.cc:1:
/usr/include/c++/8/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 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>, symbol_info>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >]’:
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, symbol_info>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, symbol_info> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../src/computation/module.H:5,
from ../src/computation/module.cc:3:
/usr/include/c++/8/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 = std::__cxx11::basic_string<char>; _Tp = symbol_info; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >]’:
/usr/include/c++/8/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>, symbol_info>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, symbol_info> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function ‘void Module::export_symbol(const symbol_info&)’:
/usr/include/c++/8/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>, symbol_info>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, symbol_info> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, symbol_info> >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function ‘void Module::import_small_decls(const Program&)’:
/usr/include/c++/8/bits/stl_map.h:892:4: note: parameter passing for argument of type ‘std::_Rb_tree_const_iterator<std::pair<const var, expression_ref> >’ changed in GCC 7.1
{ _M_t._M_insert_unique(__first, __last); }
^~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void Module::load_builtins(const module_loader&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void Module::load_constructors()’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void Module::optimize(const Program&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/module.H:7,
from ../src/computation/module.cc:3:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void Module::compile(const Program&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[115/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_machine_reroot.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_machine_reroot.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_machine_reroot.cc.o' -c ../src/computation/machine/reroot.cc
[116/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_closure.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_closure.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_closure.cc.o' -c ../src/computation/closure.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/util.H:31,
from ../src/object.H:7,
from ../src/computation/closure.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘expression_ref deindexify(const closure&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[117/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_operations.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_operations.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_operations.cc.o' -c ../src/computation/operations.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/operations.H:4,
from ../src/computation/operations.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘closure apply_op(OperationArgs&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[118/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_optimization_let-float.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_optimization_let-float.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_optimization_let-float.cc.o' -c ../src/computation/optimization/let-float.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/optimization/let-float.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair<var, expression_ref>&}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/optimization/let-float.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘expression_ref move_lets(bool, expression_ref, std::vector<std::pair<var, expression_ref> >&, const std::set<var>&, const std::set<var>&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/optimization/let-float.cc:1:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[119/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_context.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_context.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_context.cc.o' -c ../src/computation/context.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/closure.H:4,
from ../src/computation/context.H:4,
from ../src/computation/context.cc:4:
/usr/include/c++/8/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/closure.H:4,
from ../src/computation/context.H:4,
from ../src/computation/context.cc:4:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘IteratorType nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::erase(IteratorType) [with IteratorType = nlohmann::detail::iter_impl<nlohmann::basic_json<> >; typename std::enable_if<(std::is_same<InputIT, nlohmann::detail::iter_impl<nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > >::value || std::is_same<InputIT, nlohmann::detail::iter_impl<const nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > >::value), int>::type <anonymous> = 0; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’:
/usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/closure.H:4,
from ../src/computation/context.H:4,
from ../src/computation/context.cc:4:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {bool&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘BasicJsonType* nlohmann::detail::json_sax_dom_parser<BasicJsonType>::handle_value(Value&&) [with Value = bool&; BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:60,
from ../src/util.H:37,
from ../src/object.H:7,
from ../src/computation/closure.H:7,
from ../src/computation/context.H:4,
from ../src/computation/context.cc:4:
/usr/include/c++/8/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>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<void>; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../src/util.H:37,
from ../src/object.H:7,
from ../src/computation/closure.H:7,
from ../src/computation/context.H:4,
from ../src/computation/context.cc:4:
/usr/include/c++/8/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 = std::__cxx11::basic_string<char>; _Tp = nlohmann::basic_json<>; _Compare = std::less<void>; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/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>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function ‘bool nlohmann::detail::json_sax_dom_callback_parser<BasicJsonType>::key(nlohmann::detail::json_sax_dom_callback_parser<BasicJsonType>::string_t&) [with BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/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>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/closure.H:4,
from ../src/computation/context.H:4,
from ../src/computation/context.cc:4:
/usr/include/c++/8/bits/vector.tcc: In member function ‘bool nlohmann::detail::parser<BasicJsonType>::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser<nlohmann::basic_json<> >; BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[120/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_loader.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_loader.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_loader.cc.o' -c ../src/computation/loader.cc
[121/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_program.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_program.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_program.cc.o' -c ../src/computation/program.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/program.H:4,
from ../src/computation/program.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Module&}; _Tp = Module; _Alloc = std::allocator<Module>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<Module>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<Module*, std::vector<Module> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {Module}; _Tp = Module; _Alloc = std::allocator<Module>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<Module>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<Module*, std::vector<Module> >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void Program::add(const string&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Module*, std::vector<Module> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/program.H:4,
from ../src/computation/program.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘void Program::add(const Module&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<Module*, std::vector<Module> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[122/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/mcmc_sample-tri.cc.o' -MF 'src/25a6634@@bali-phy@exe/mcmc_sample-tri.cc.o.d' -o 'src/25a6634@@bali-phy@exe/mcmc_sample-tri.cc.o' -c ../src/mcmc/sample-tri.cc
[123/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/startup_system.cc.o' -MF 'src/25a6634@@bali-phy@exe/startup_system.cc.o.d' -o 'src/25a6634@@bali-phy@exe/startup_system.cc.o' -c ../src/startup/system.cc
[124/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/startup_files.cc.o' -MF 'src/25a6634@@bali-phy@exe/startup_files.cc.o.d' -o 'src/25a6634@@bali-phy@exe/startup_files.cc.o' -c ../src/startup/files.cc
In file included from /usr/include/c++/8/vector:69,
from /usr/include/boost/filesystem/path_traits.hpp:26,
from /usr/include/boost/filesystem/path.hpp:25,
from /usr/include/boost/filesystem/operations.hpp:25,
from ../src/startup/files.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘void run_info(nlohmann::json&, int, int, char**)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[125/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/startup_A-T-model.cc.o' -MF 'src/25a6634@@bali-phy@exe/startup_A-T-model.cc.o.d' -o 'src/25a6634@@bali-phy@exe/startup_A-T-model.cc.o' -c ../src/startup/A-T-model.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/startup/A-T-model.H:4,
from ../src/startup/A-T-model.cc:1:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/startup/A-T-model.H:4,
from ../src/startup/A-T-model.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘void setup_heating(int, const boost::program_options::variables_map&, Parameters&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/startup/A-T-model.H:4,
from ../src/startup/A-T-model.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::push_back(nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>&&) [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/startup/A-T-model.H:4,
from ../src/startup/A-T-model.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘nlohmann::json log_summary(std::ostream&, std::ostream&, std::ostream&, const std::vector<model_t>&, const std::vector<model_t>&, const std::vector<model_t>&, const model_t&, const Parameters&, const boost::program_options::variables_map&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/startup/A-T-model.H:4,
from ../src/startup/A-T-model.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {model_t}; _Tp = model_t; _Alloc = std::allocator<model_t>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<model_t>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<model_t*, std::vector<model_t> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘std::vector<model_t> get_imodels(const Rules&, const shared_items<std::__cxx11::basic_string<char> >&, const SequenceTree&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<model_t*, std::vector<model_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘owned_ptr<Model> create_A_and_T_model(const Rules&, boost::program_options::variables_map&, const std::shared_ptr<module_loader>&, std::ostream&, std::ostream&, std::ostream&, nlohmann::json&, int)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<model_t*, std::vector<model_t> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[126/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/startup_loggers.cc.o' -MF 'src/25a6634@@bali-phy@exe/startup_loggers.cc.o.d' -o 'src/25a6634@@bali-phy@exe/startup_loggers.cc.o' -c ../src/startup/loggers.cc
[127/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_11c875020bf4f86494356c6e5f12454e39673bcc.dat
[128/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/startup_cmd_line.cc.o' -MF 'src/25a6634@@bali-phy@exe/startup_cmd_line.cc.o.d' -o 'src/25a6634@@bali-phy@exe/startup_cmd_line.cc.o' -c ../src/startup/cmd_line.cc
[129/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/models_parse.cc.o' -MF 'src/25a6634@@bali-phy@exe/models_parse.cc.o.d' -o 'src/25a6634@@bali-phy@exe/models_parse.cc.o' -c ../src/models/parse.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/models/parse.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>&}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/models/parse.cc:2:
/usr/include/c++/8/bits/stl_vector.h: In function ‘void handle_positional_args(ptree&, const Rules&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[130/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/models_rules.cc.o' -MF 'src/25a6634@@bali-phy@exe/models_rules.cc.o.d' -o 'src/25a6634@@bali-phy@exe/models_rules.cc.o' -c ../src/models/rules.cc
../src/models/rules.cc: In function ‘ptree json_to_ptree(const json&)’:
../src/models/rules.cc:304:39: warning: ‘static nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::iteration_proxy<nlohmann::detail::iter_impl<const nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > > nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::iterator_wrapper(nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::const_reference) [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer; nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::iteration_proxy<nlohmann::detail::iter_impl<const nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > > = nlohmann::detail::iteration_proxy<nlohmann::detail::iter_impl<const nlohmann::basic_json<> > >; nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::const_reference = const nlohmann::basic_json<>&; nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::value_type = nlohmann::basic_json<>]’ is deprecated [-Wdeprecated-declarations]
for(auto it: json::iterator_wrapper(j))
^
In file included from ../src/util/json.hh:3,
from ../src/util/ptree.H:12,
from ../src/models/rules.H:6,
from ../src/models/rules.cc:3:
/usr/include/nlohmann/json.hpp:4308:44: note: declared here
static iteration_proxy<const_iterator> iterator_wrapper(const_reference ref) noexcept
^~~~~~~~~~~~~~~~
../src/models/rules.cc:304:39: warning: ‘static nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::iteration_proxy<nlohmann::detail::iter_impl<const nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > > nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::iterator_wrapper(nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::const_reference) [with ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer; nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::iteration_proxy<nlohmann::detail::iter_impl<const nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > > = nlohmann::detail::iteration_proxy<nlohmann::detail::iter_impl<const nlohmann::basic_json<> > >; nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::const_reference = const nlohmann::basic_json<>&; nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::value_type = nlohmann::basic_json<>]’ is deprecated [-Wdeprecated-declarations]
for(auto it: json::iterator_wrapper(j))
^
In file included from ../src/util/json.hh:3,
from ../src/util/ptree.H:12,
from ../src/models/rules.H:6,
from ../src/models/rules.cc:3:
/usr/include/nlohmann/json.hpp:4308:44: note: declared here
static iteration_proxy<const_iterator> iterator_wrapper(const_reference ref) noexcept
^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/models/rules.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘ptree parse_constraints(const ptree&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/models/rules.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘IteratorType nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer>::erase(IteratorType) [with IteratorType = nlohmann::detail::iter_impl<nlohmann::basic_json<> >; typename std::enable_if<(std::is_same<InputIT, nlohmann::detail::iter_impl<nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > >::value || std::is_same<InputIT, nlohmann::detail::iter_impl<const nlohmann::basic_json<ObjectType, ArrayType, StringType, BooleanType, NumberIntegerType, NumberUnsignedType, NumberFloatType, AllocatorType, JSONSerializer> > >::value), int>::type <anonymous> = 0; ObjectType = std::map; ArrayType = std::vector; StringType = std::__cxx11::basic_string<char>; BooleanType = bool; NumberIntegerType = long long int; NumberUnsignedType = long long unsigned int; NumberFloatType = double; AllocatorType = std::allocator; JSONSerializer = nlohmann::adl_serializer]’:
/usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
{ return _M_erase(begin() + (__position - cbegin())); }
^
In file included from /usr/include/c++/8/vector:69,
from ../src/models/rules.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::detail::value_t}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::start_object(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘bool nlohmann::detail::json_sax_dom_parser<BasicJsonType>::start_array(std::size_t) [with BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {bool&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘BasicJsonType* nlohmann::detail::json_sax_dom_parser<BasicJsonType>::handle_value(Value&&) [with Value = bool&; BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int&}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {nlohmann::basic_json<std::map, std::vector, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, long long int, long long unsigned int, double, std::allocator, nlohmann::adl_serializer>}; _Tp = nlohmann::basic_json<>; _Alloc = std::allocator<nlohmann::basic_json<> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/set:60,
from ../src/models/rules.cc:2:
/usr/include/c++/8/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>, nlohmann::basic_json<> >; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >; _Compare = std::less<void>; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/bits/stl_tree.h:2411:7: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/map:61,
from ../src/models/rules.H:5,
from ../src/models/rules.cc:3:
/usr/include/c++/8/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 = std::__cxx11::basic_string<char>; _Tp = nlohmann::basic_json<>; _Compare = std::less<void>; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >]’:
/usr/include/c++/8/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>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
/usr/include/c++/8/bits/stl_map.h: In member function ‘bool nlohmann::detail::json_sax_dom_callback_parser<BasicJsonType>::key(nlohmann::detail::json_sax_dom_callback_parser<BasicJsonType>::string_t&) [with BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/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>, nlohmann::basic_json<> >, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >, std::less<void>, std::allocator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, nlohmann::basic_json<> > >’} changed in GCC 7.1
__i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct,
In file included from /usr/include/c++/8/vector:69,
from ../src/models/rules.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘bool nlohmann::detail::parser<BasicJsonType>::sax_parse_internal(SAX*) [with SAX = nlohmann::detail::json_sax_dom_parser<nlohmann::basic_json<> >; BasicJsonType = nlohmann::basic_json<>]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<nlohmann::basic_json<>*, std::vector<nlohmann::basic_json<>, std::allocator<nlohmann::basic_json<> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[131/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/models_unification.cc.o' -MF 'src/25a6634@@bali-phy@exe/models_unification.cc.o.d' -o 'src/25a6634@@bali-phy@exe/models_unification.cc.o' -c ../src/models/unification.cc
In file included from /usr/include/c++/8/set:60,
from ../src/models/unification.H:5,
from ../src/models/unification.cc:1:
/usr/include/c++/8/bits/stl_tree.h: In member function ‘std::pair<std::_Rb_tree_node_base*, std::_Rb_tree_node_base*> std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, const key_type&) [with _Key = std::__cxx11::basic_string<char>; _Val = std::pair<const std::__cxx11::basic_string<char>, ptree>; _KeyOfValue = std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ptree> >; _Compare = std::less<std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<const std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/stl_tree.h:2146:5: note: parameter passing for argument of type ‘std::_Rb_tree<std::__cxx11::basic_string<char>, std::pair<const std::__cxx11::basic_string<char>, ptree>, std::_Select1st<std::pair<const std::__cxx11::basic_string<char>, ptree> >, std::less<std::__cxx11::basic_string<char> >, std::allocator<std::pair<const std::__cxx11::basic_string<char>, ptree> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator<std::pair<const std::__cxx11::basic_string<char>, ptree> >’} changed in GCC 7.1
_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[132/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/models_translate.cc.o' -MF 'src/25a6634@@bali-phy@exe/models_translate.cc.o.d' -o 'src/25a6634@@bali-phy@exe/models_translate.cc.o' -c ../src/models/translate.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/models/translate.H:4,
from ../src/models/translate.cc:1:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>&}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ptree>}; _Tp = std::pair<std::__cxx11::basic_string<char>, ptree>; _Alloc = std::allocator<std::pair<std::__cxx11::basic_string<char>, ptree> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > extend_scope(const ptree&, int, const std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/models/translate.H:4,
from ../src/models/translate.cc:1:
/usr/include/c++/8/bits/stl_vector.h: In function ‘equations pass2(const Rules&, const ptree&, ptree&, std::set<std::__cxx11::basic_string<char> >, const std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> >&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<std::__cxx11::basic_string<char>, ptree>*, std::vector<std::pair<std::__cxx11::basic_string<char>, ptree> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[133/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/startup_paths.cc.o' -MF 'src/25a6634@@bali-phy@exe/startup_paths.cc.o.d' -o 'src/25a6634@@bali-phy@exe/startup_paths.cc.o' -c ../src/startup/paths.cc
[134/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_expression_bool.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_expression_bool.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_expression_bool.cc.o' -c ../src/computation/expression/bool.cc
[135/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_optimization_inliner.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_optimization_inliner.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_optimization_inliner.cc.o' -c ../src/computation/optimization/inliner.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/operations.H:4,
from ../src/computation/optimization/inliner.cc:4:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/operations.H:4,
from ../src/computation/optimization/inliner.cc:4:
/usr/include/c++/8/bits/stl_vector.h: In function ‘inline_context unknown_context()’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘inline_context argument_context(const inline_context&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘inline_context case_object_context(expression_ref, const inline_context&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘inline_context apply_object_context_one_arg(const inline_context&, const expression_ref&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[136/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_optimization_simplifier.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_optimization_simplifier.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_optimization_simplifier.cc.o' -c ../src/computation/optimization/simplifier.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/operations.H:4,
from ../src/computation/optimization/simplifier.cc:4:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair<var, expression_ref>&}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair<var, expression_ref>}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/operations.H:4,
from ../src/computation/optimization/simplifier.cc:4:
/usr/include/c++/8/bits/stl_vector.h: In function ‘substitution simplify_decls(const simplifier_options&, CDecls&, const substitution&, in_scope_set&, bool)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[137/256] c++ -Isrc/builtins/2382537@@Array@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Array@sha/Array.cc.o' -MF 'src/builtins/2382537@@Array@sha/Array.cc.o.d' -o 'src/builtins/2382537@@Array@sha/Array.cc.o' -c ../src/builtins/Array.cc
[138/256] c++ -o src/builtins/Array.so 'src/builtins/2382537@@Array@sha/Array.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Array.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[139/256] c++ -Isrc/builtins/2382537@@Alphabet@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Alphabet@sha/Alphabet.cc.o' -MF 'src/builtins/2382537@@Alphabet@sha/Alphabet.cc.o.d' -o 'src/builtins/2382537@@Alphabet@sha/Alphabet.cc.o' -c ../src/builtins/Alphabet.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/../util.H:31,
from ../src/builtins/../object.H:7,
from ../src/builtins/../computation/machine/args.H:4,
from ../src/builtins/Alphabet.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘closure builtin_function_alphabet_letters(OperationArgs&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[140/256] c++ -Isrc/builtins/2382537@@Prelude@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Prelude@sha/Prelude.cc.o' -MF 'src/builtins/2382537@@Prelude@sha/Prelude.cc.o.d' -o 'src/builtins/2382537@@Prelude@sha/Prelude.cc.o' -c ../src/builtins/Prelude.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/../util.H:31,
from ../src/builtins/../object.H:7,
from ../src/builtins/../computation/machine/args.H:4,
from ../src/builtins/Prelude.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/builtins/../util.H:31,
from ../src/builtins/../object.H:7,
from ../src/builtins/../computation/machine/args.H:4,
from ../src/builtins/Prelude.cc:2:
/usr/include/c++/8/bits/stl_vector.h: In function ‘closure builtin_function_vector_from_list(OperationArgs&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘closure builtin_function_error(OperationArgs&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[141/256] c++ -o src/builtins/Prelude.so 'src/builtins/2382537@@Prelude@sha/Prelude.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Prelude.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[142/256] c++ -o src/builtins/Alphabet.so 'src/builtins/2382537@@Alphabet@sha/Alphabet.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Alphabet.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[143/256] c++ -Isrc/25a6634@@bali-phy@exe -Isrc -I../src -I. -I../ -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-phy@exe/computation_optimization_occurrence.cc.o' -MF 'src/25a6634@@bali-phy@exe/computation_optimization_occurrence.cc.o.d' -o 'src/25a6634@@bali-phy@exe/computation_optimization_occurrence.cc.o' -c ../src/computation/optimization/occurrence.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/computation/operations.H:4,
from ../src/computation/optimization/occurrence.cc:4:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const std::pair<var, expression_ref>&}; _Tp = std::pair<var, expression_ref>; _Alloc = std::allocator<std::pair<var, expression_ref> >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<var, expression_ref> >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’} changed in GCC 7.1
In file included from /usr/include/c++/8/vector:64,
from ../src/computation/operations.H:4,
from ../src/computation/optimization/occurrence.cc:4:
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::vector<std::vector<std::pair<var, expression_ref> > > occurrence_analyze_decls(CDecls, std::set<var>&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<var, expression_ref>*, std::vector<std::pair<var, expression_ref> > >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘std::pair<expression_ref, std::set<var> > occurrence_analyzer(const expression_ref&, var_context)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[144/256] c++ -Isrc/builtins/2382537@@Data@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Data@sha/Data.cc.o' -MF 'src/builtins/2382537@@Data@sha/Data.cc.o.d' -o 'src/builtins/2382537@@Data@sha/Data.cc.o' -c ../src/builtins/Data.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/Data.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘closure builtin_function_read_file(OperationArgs&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[145/256] c++ -o src/builtins/Data.so 'src/builtins/2382537@@Data@sha/Data.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Data.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[146/256] c++ -Isrc/builtins/2382537@@Pair@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Pair@sha/Pair.cc.o' -MF 'src/builtins/2382537@@Pair@sha/Pair.cc.o.d' -o 'src/builtins/2382537@@Pair@sha/Pair.cc.o' -c ../src/builtins/Pair.cc
[147/256] c++ -o src/bali-phy 'src/25a6634@@bali-phy@exe/dp_dp_hmm.cc.o' 'src/25a6634@@bali-phy@exe/parser_desugar.cc.o' 'src/25a6634@@bali-phy@exe/parser_desugar-case.cc.o' 'src/25a6634@@bali-phy@exe/parser_rename.cc.o' 'src/25a6634@@bali-phy@exe/parser_driver.cc.o' 'src/25a6634@@bali-phy@exe/parser_lexer.cc.o' 'src/25a6634@@bali-phy@exe/parser_parser.cc.o' 'src/25a6634@@bali-phy@exe/substitution_substitution.cc.o' 'src/25a6634@@bali-phy@exe/util_ptree.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_moves.cc.o' 'src/25a6634@@bali-phy@exe/math_exponential.cc.o' 'src/25a6634@@bali-phy@exe/math_eigenvalue.cc.o' 'src/25a6634@@bali-phy@exe/models_parameters.cc.o' 'src/25a6634@@bali-phy@exe/prior.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_mcmc.cc.o' 'src/25a6634@@bali-phy@exe/probability_choose.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_sample-branch-lengths.cc.o' 'src/25a6634@@bali-phy@exe/bali-phy.cc.o' 'src/25a6634@@bali-phy@exe/util_text.cc.o' 'src/25a6634@@bali-phy@exe/models_TreeInterface.cc.o' 'src/25a6634@@bali-phy@exe/dp_hmm.cc.o' 'src/25a6634@@bali-phy@exe/dp_dp-engine.cc.o' 'src/25a6634@@bali-phy@exe/dp_dp-array.cc.o' 'src/25a6634@@bali-phy@exe/dp_dp-matrix.cc.o' 'src/25a6634@@bali-phy@exe/dp_3way.cc.o' 'src/25a6634@@bali-phy@exe/dp_2way.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_sample-alignment.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_sample-node.cc.o' 'src/25a6634@@bali-phy@exe/imodel_imodel.cc.o' 'src/25a6634@@bali-phy@exe/dp_5way.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_sample-topology-NNI.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_sample-two-nodes.cc.o' 'src/25a6634@@bali-phy@exe/dp_dp-cube.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_sample-cube.cc.o' 'src/25a6634@@bali-phy@exe/models_setup.cc.o' 'src/25a6634@@bali-phy@exe/startup_help.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_sample-topology-SPR.cc.o' 'src/25a6634@@bali-phy@exe/dp_alignment-sums.cc.o' 'src/25a6634@@bali-phy@exe/probability_probability.cc.o' 'src/25a6634@@bali-phy@exe/models_model.cc.o' 'src/25a6634@@bali-phy@exe/alignment_alignment-constraint.cc.o' 'src/25a6634@@bali-phy@exe/monitor.cc.o' 'src/25a6634@@bali-phy@exe/myexception.cc.o' 'src/25a6634@@bali-phy@exe/math_pow2.cc.o' 'src/25a6634@@bali-phy@exe/substitution_parsimony.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_proposals.cc.o' 'src/25a6634@@bali-phy@exe/n_indels2.cc.o' 'src/25a6634@@bali-phy@exe/alignment_alignment-util2.cc.o' 'src/25a6634@@bali-phy@exe/tools_parsimony2.cc.o' 'src/25a6634@@bali-phy@exe/version.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_slice-sampling.cc.o' 'src/25a6634@@bali-phy@exe/timer_stack.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_setup.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_logger.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_AIS.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_operator.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_expression.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_constructor.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_expression_ref.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_AST_node.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_apply.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_substitute.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_indexify.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_let.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_case.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_trim.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_tuple.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_list.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_var.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_lambda.cc.o' 'src/25a6634@@bali-phy@exe/computation_machine_args.cc.o' 'src/25a6634@@bali-phy@exe/computation_machine_tokens.cc.o' 'src/25a6634@@bali-phy@exe/computation_preprocess.cc.o' 'src/25a6634@@bali-phy@exe/computation_machine_graph_register.cc.o' 'src/25a6634@@bali-phy@exe/computation_machine_show_graph.cc.o' 'src/25a6634@@bali-phy@exe/computation_module.cc.o' 'src/25a6634@@bali-phy@exe/computation_machine_evaluate.cc.o' 'src/25a6634@@bali-phy@exe/computation_machine_gc.cc.o' 'src/25a6634@@bali-phy@exe/computation_machine_reroot.cc.o' 'src/25a6634@@bali-phy@exe/computation_operations.cc.o' 'src/25a6634@@bali-phy@exe/computation_loader.cc.o' 'src/25a6634@@bali-phy@exe/computation_context.cc.o' 'src/25a6634@@bali-phy@exe/computation_closure.cc.o' 'src/25a6634@@bali-phy@exe/computation_optimization_let-float.cc.o' 'src/25a6634@@bali-phy@exe/computation_program.cc.o' 'src/25a6634@@bali-phy@exe/mcmc_sample-tri.cc.o' 'src/25a6634@@bali-phy@exe/startup_A-T-model.cc.o' 'src/25a6634@@bali-phy@exe/startup_files.cc.o' 'src/25a6634@@bali-phy@exe/startup_loggers.cc.o' 'src/25a6634@@bali-phy@exe/startup_system.cc.o' 'src/25a6634@@bali-phy@exe/startup_cmd_line.cc.o' 'src/25a6634@@bali-phy@exe/models_rules.cc.o' 'src/25a6634@@bali-phy@exe/models_parse.cc.o' 'src/25a6634@@bali-phy@exe/models_translate.cc.o' 'src/25a6634@@bali-phy@exe/models_unification.cc.o' 'src/25a6634@@bali-phy@exe/computation_optimization_simplifier.cc.o' 'src/25a6634@@bali-phy@exe/startup_paths.cc.o' 'src/25a6634@@bali-phy@exe/computation_optimization_occurrence.cc.o' 'src/25a6634@@bali-phy@exe/computation_optimization_inliner.cc.o' 'src/25a6634@@bali-phy@exe/computation_expression_bool.cc.o' -Wl,--no-undefined -Wl,--as-needed -Wl,-export-dynamic -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a src/liblibsums.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -ldl -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[148/256] c++ -o src/builtins/Pair.so 'src/builtins/2382537@@Pair@sha/Pair.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Pair.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[149/256] c++ -Isrc/builtins/2382537@@Modifiables@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Modifiables@sha/Modifiables.cc.o' -MF 'src/builtins/2382537@@Modifiables@sha/Modifiables.cc.o.d' -o 'src/builtins/2382537@@Modifiables@sha/Modifiables.cc.o' -c ../src/builtins/Modifiables.cc
[150/256] c++ -o src/builtins/Modifiables.so 'src/builtins/2382537@@Modifiables@sha/Modifiables.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Modifiables.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[151/256] c++ -Isrc/builtins/2382537@@PopGen@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@PopGen@sha/PopGen.cc.o' -MF 'src/builtins/2382537@@PopGen@sha/PopGen.cc.o.d' -o 'src/builtins/2382537@@PopGen@sha/PopGen.cc.o' -c ../src/builtins/PopGen.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/PopGen.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/builtins/PopGen.cc:3:
/usr/include/c++/8/bits/stl_vector.h: In function ‘closure builtin_function_remove_2nd_allele(OperationArgs&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/PopGen.cc:3:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘closure builtin_function_read_phase_file(OperationArgs&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘closure builtin_function_allele_frequency_spectrum(OperationArgs&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[152/256] c++ -Isrc/builtins/2382537@@Distribution@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Distribution@sha/Distribution.cc.o' -MF 'src/builtins/2382537@@Distribution@sha/Distribution.cc.o.d' -o 'src/builtins/2382537@@Distribution@sha/Distribution.cc.o' -c ../src/builtins/Distribution.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/Distribution.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const expression_ref&}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/builtins/Distribution.cc:2:
/usr/include/c++/8/bits/stl_vector.h: In function ‘closure builtin_function_CRP_density(OperationArgs&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘closure builtin_function_sample_categorical(OperationArgs&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/Distribution.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘closure builtin_function_sample_CRP(OperationArgs&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[153/256] c++ -o src/builtins/PopGen.so 'src/builtins/2382537@@PopGen@sha/PopGen.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,PopGen.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[154/256] c++ -o src/builtins/Distribution.so 'src/builtins/2382537@@Distribution@sha/Distribution.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Distribution.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[155/256] c++ -Isrc/builtins/2382537@@Alignment@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Alignment@sha/Alignment.cc.o' -MF 'src/builtins/2382537@@Alignment@sha/Alignment.cc.o.d' -o 'src/builtins/2382537@@Alignment@sha/Alignment.cc.o' -c ../src/builtins/Alignment.cc
[156/256] c++ -o src/builtins/Alignment.so 'src/builtins/2382537@@Alignment@sha/Alignment.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Alignment.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[157/256] c++ -Isrc/builtins/2382537@@Range@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Range@sha/Range.cc.o' -MF 'src/builtins/2382537@@Range@sha/Range.cc.o.d' -o 'src/builtins/2382537@@Range@sha/Range.cc.o' -c ../src/builtins/Range.cc
[158/256] c++ -o src/builtins/Range.so 'src/builtins/2382537@@Range@sha/Range.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Range.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[159/256] c++ -Isrc/builtins/2382537@@SModel@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@SModel@sha/SModel.cc.o' -MF 'src/builtins/2382537@@SModel@sha/SModel.cc.o.d' -o 'src/builtins/2382537@@SModel@sha/SModel.cc.o' -c ../src/builtins/SModel.cc
[160/256] c++ -o src/builtins/SModel.so 'src/builtins/2382537@@SModel@sha/SModel.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,SModel.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[161/256] c++ -Isrc/builtins/2382537@@MCMC@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@MCMC@sha/MCMC.cc.o' -MF 'src/builtins/2382537@@MCMC@sha/MCMC.cc.o.d' -o 'src/builtins/2382537@@MCMC@sha/MCMC.cc.o' -c ../src/builtins/MCMC.cc
[162/256] c++ -o src/builtins/MCMC.so 'src/builtins/2382537@@MCMC@sha/MCMC.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,MCMC.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[163/256] c++ -Isrc/builtins/2382537@@Vector@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Vector@sha/Vector.cc.o' -MF 'src/builtins/2382537@@Vector@sha/Vector.cc.o.d' -o 'src/builtins/2382537@@Vector@sha/Vector.cc.o' -c ../src/builtins/Vector.cc
[164/256] c++ -o src/builtins/Vector.so 'src/builtins/2382537@@Vector@sha/Vector.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Vector.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[165/256] c++ -Isrc/builtins/2382537@@Environment@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Environment@sha/Environment.cc.o' -MF 'src/builtins/2382537@@Environment@sha/Environment.cc.o.d' -o 'src/builtins/2382537@@Environment@sha/Environment.cc.o' -c ../src/builtins/Environment.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/../util.H:31,
from ../src/builtins/../object.H:7,
from ../src/builtins/../computation/machine/args.H:4,
from ../src/builtins/Environment.cc:2:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {expression_ref}; _Tp = expression_ref; _Alloc = std::allocator<expression_ref>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<expression_ref>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘closure builtin_function_getArgs(OperationArgs&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<expression_ref*, std::vector<expression_ref> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[166/256] c++ -o src/builtins/Environment.so 'src/builtins/2382537@@Environment@sha/Environment.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Environment.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[167/256] c++ -Isrc/builtins/2382537@@Real@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@Real@sha/Real.cc.o' -MF 'src/builtins/2382537@@Real@sha/Real.cc.o.d' -o 'src/builtins/2382537@@Real@sha/Real.cc.o' -c ../src/builtins/Real.cc
[168/256] c++ -o src/builtins/Real.so 'src/builtins/2382537@@Real@sha/Real.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,Real.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[169/256] c++ -Isrc/25a6634@@model_P@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@model_P@exe/tools_model_P.cc.o' -MF 'src/25a6634@@model_P@exe/tools_model_P.cc.o.d' -o 'src/25a6634@@model_P@exe/tools_model_P.cc.o' -c ../src/tools/model_P.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/tools/model_P.cc:21:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/tools/model_P.cc:21:
/usr/include/c++/8/bits/stl_vector.h: In function ‘int main(int, char**)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[170/256] c++ -o src/model_P 'src/25a6634@@model_P@exe/tools_model_P.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[171/256] c++ -Isrc/builtins/2382537@@SMC@sha -Isrc/builtins -I../src/builtins -Isrc/builtins/.. -I../src/builtins/.. -I/usr/include/eigen3 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -MD -MQ 'src/builtins/2382537@@SMC@sha/SMC.cc.o' -MF 'src/builtins/2382537@@SMC@sha/SMC.cc.o.d' -o 'src/builtins/2382537@@SMC@sha/SMC.cc.o' -c ../src/builtins/SMC.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/builtins/SMC.cc:3:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘log_double_t smc(double, std::vector<double>, std::vector<double>, const alignment&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘closure builtin_function_smc_density(OperationArgs&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[172/256] c++ -Isrc/25a6634@@stats-select@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@stats-select@exe/tools_stats-select.cc.o' -MF 'src/25a6634@@stats-select@exe/tools_stats-select.cc.o.d' -o 'src/25a6634@@stats-select@exe/tools_stats-select.cc.o' -c ../src/tools/stats-select.cc
[173/256] c++ -o src/builtins/SMC.so 'src/builtins/2382537@@SMC@sha/SMC.cc.o' -Wl,--as-needed -shared -fPIC -Wl,--start-group -Wl,-soname,SMC.so -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group
[174/256] c++ -o src/stats-select 'src/25a6634@@stats-select@exe/tools_stats-select.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[175/256] c++ -Isrc/25a6634@@statreport@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@statreport@exe/tools_statreport.cc.o' -MF 'src/25a6634@@statreport@exe/tools_statreport.cc.o.d' -o 'src/25a6634@@statreport@exe/tools_statreport.cc.o' -c ../src/tools/statreport.cc
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../src/util.H:34,
from ../src/tools/statreport.cc:30:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../src/util.H:34,
from ../src/tools/statreport.cc:30:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/tools/statreport.cc:27:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/tools/statreport.cc:27:
/usr/include/c++/8/bits/stl_vector.h: In function ‘int get_burn_in(const std::vector<double>&, double, int)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../src/util.H:34,
from ../src/tools/statreport.cc:30:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘void show_median(boost::program_options::variables_map&, const string&, const std::vector<Table<double> >&, int, const std::vector<double>&, bool, double&, double&, double&)’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/tools/statreport.cc:27:
/usr/include/c++/8/bits/stl_vector.h: In function ‘int main(int, char**)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../src/util.H:34,
from ../src/tools/statreport.cc:30:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[176/256] c++ -o src/statreport 'src/25a6634@@statreport@exe/tools_statreport.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[177/256] c++ -Isrc/25a6634@@alignment-gild@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-gild@exe/tools_alignment-gild.cc.o' -MF 'src/25a6634@@alignment-gild@exe/tools_alignment-gild.cc.o.d' -o 'src/25a6634@@alignment-gild@exe/tools_alignment-gild.cc.o' -c ../src/tools/alignment-gild.cc
[178/256] c++ -Isrc/25a6634@@alignment-chop-internal@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-chop-internal@exe/tools_alignment-chop-internal.cc.o' -MF 'src/25a6634@@alignment-chop-internal@exe/tools_alignment-chop-internal.cc.o.d' -o 'src/25a6634@@alignment-chop-internal@exe/tools_alignment-chop-internal.cc.o' -c ../src/tools/alignment-chop-internal.cc
[179/256] c++ -o src/alignment-gild 'src/25a6634@@alignment-gild@exe/tools_alignment-gild.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[180/256] c++ -Isrc/25a6634@@alignment-consensus@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-consensus@exe/tools_alignment-consensus.cc.o' -MF 'src/25a6634@@alignment-consensus@exe/tools_alignment-consensus.cc.o.d' -o 'src/25a6634@@alignment-consensus@exe/tools_alignment-consensus.cc.o' -c ../src/tools/alignment-consensus.cc
[181/256] c++ -o src/alignment-chop-internal 'src/25a6634@@alignment-chop-internal@exe/tools_alignment-chop-internal.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[182/256] c++ -o src/alignment-consensus 'src/25a6634@@alignment-consensus@exe/tools_alignment-consensus.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[183/256] c++ -Isrc/25a6634@@alignment-max@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-max@exe/tools_alignment-max.cc.o' -MF 'src/25a6634@@alignment-max@exe/tools_alignment-max.cc.o.d' -o 'src/25a6634@@alignment-max@exe/tools_alignment-max.cc.o' -c ../src/tools/alignment-max.cc
[184/256] c++ -o src/alignment-max 'src/25a6634@@alignment-max@exe/tools_alignment-max.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[185/256] c++ -Isrc/25a6634@@alignment-find@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-find@exe/tools_alignment-find.cc.o' -MF 'src/25a6634@@alignment-find@exe/tools_alignment-find.cc.o.d' -o 'src/25a6634@@alignment-find@exe/tools_alignment-find.cc.o' -c ../src/tools/alignment-find.cc
[186/256] c++ -Isrc/25a6634@@alignment-info@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-info@exe/tools_alignment-info.cc.o' -MF 'src/25a6634@@alignment-info@exe/tools_alignment-info.cc.o.d' -o 'src/25a6634@@alignment-info@exe/tools_alignment-info.cc.o' -c ../src/tools/alignment-info.cc
[187/256] c++ -o src/alignment-info 'src/25a6634@@alignment-info@exe/tools_alignment-info.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[188/256] c++ -Isrc/25a6634@@alignment-indices@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-indices@exe/tools_alignment-indices.cc.o' -MF 'src/25a6634@@alignment-indices@exe/tools_alignment-indices.cc.o.d' -o 'src/25a6634@@alignment-indices@exe/tools_alignment-indices.cc.o' -c ../src/tools/alignment-indices.cc
[189/256] c++ -o src/alignment-indices 'src/25a6634@@alignment-indices@exe/tools_alignment-indices.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[190/256] c++ -o src/alignment-find 'src/25a6634@@alignment-find@exe/tools_alignment-find.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[191/256] c++ -Isrc/25a6634@@alignment-translate@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-translate@exe/tools_alignment-translate.cc.o' -MF 'src/25a6634@@alignment-translate@exe/tools_alignment-translate.cc.o.d' -o 'src/25a6634@@alignment-translate@exe/tools_alignment-translate.cc.o' -c ../src/tools/alignment-translate.cc
[192/256] c++ -o src/alignment-translate 'src/25a6634@@alignment-translate@exe/tools_alignment-translate.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[193/256] c++ -Isrc/25a6634@@tree-mean-lengths@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@tree-mean-lengths@exe/tools_tree-mean-lengths.cc.o' -MF 'src/25a6634@@tree-mean-lengths@exe/tools_tree-mean-lengths.cc.o.d' -o 'src/25a6634@@tree-mean-lengths@exe/tools_tree-mean-lengths.cc.o' -c ../src/tools/tree-mean-lengths.cc
[194/256] c++ -o src/tree-mean-lengths 'src/25a6634@@tree-mean-lengths@exe/tools_tree-mean-lengths.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[195/256] c++ -Isrc/25a6634@@alignment-cat@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-cat@exe/tools_alignment-cat.cc.o' -MF 'src/25a6634@@alignment-cat@exe/tools_alignment-cat.cc.o.d' -o 'src/25a6634@@alignment-cat@exe/tools_alignment-cat.cc.o' -c ../src/tools/alignment-cat.cc
[196/256] c++ -o src/alignment-cat 'src/25a6634@@alignment-cat@exe/tools_alignment-cat.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[197/256] c++ -Isrc/25a6634@@trees-consensus@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@trees-consensus@exe/tools_trees-consensus.cc.o' -MF 'src/25a6634@@trees-consensus@exe/tools_trees-consensus.cc.o.d' -o 'src/25a6634@@trees-consensus@exe/tools_trees-consensus.cc.o' -c ../src/tools/trees-consensus.cc
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../src/tools/trees-consensus.cc:21:
/usr/include/c++/8/bits/stl_heap.h: In function ‘void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >; _Distance = int; _Tp = std::pair<double, std::__cxx11::basic_string<char> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<consensus_level_order>]’:
/usr/include/c++/8/bits/stl_heap.h:214:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../src/tools/trees-consensus.cc:21:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<consensus_level_order>]’:
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
In file included from /usr/include/c++/8/vector:69,
from ../src/tools/trees-consensus.cc:23:
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<double, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >}; _Tp = std::pair<double, std::__cxx11::basic_string<char> >; _Alloc = std::allocator<std::pair<double, std::__cxx11::basic_string<char> > >]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<std::pair<double, std::__cxx11::basic_string<char> > >::iterator’ {aka ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’} changed in GCC 7.1
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../src/tools/trees-consensus.cc:21:
/usr/include/c++/8/bits/stl_heap.h: In function ‘void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<consensus_level_order>]’:
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
__make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
^~~~~~~~~~~
/usr/include/c++/8/bits/stl_heap.h:326:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
In file included from /usr/include/c++/8/algorithm:62,
from ../src/tools/trees-consensus.cc:21:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<consensus_level_order>]’:
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1672:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
std::__make_heap(__first, __middle, __comp);
~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/tools/trees-consensus.cc:23:
/usr/include/c++/8/bits/vector.tcc: In function ‘std::vector<std::pair<double, std::__cxx11::basic_string<char> > > get_consensus_levels(const string&)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../src/tools/trees-consensus.cc:21:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:69,
from ../src/tools/trees-consensus.cc:23:
/usr/include/c++/8/bits/vector.tcc: In function ‘int main(int, char**)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<std::pair<double, std::__cxx11::basic_string<char> >*, std::vector<std::pair<double, std::__cxx11::basic_string<char> > > >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[198/256] c++ -o src/trees-consensus 'src/25a6634@@trees-consensus@exe/tools_trees-consensus.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[199/256] c++ -Isrc/25a6634@@mctree-mean-lengths@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@mctree-mean-lengths@exe/tools_mctree-mean-lengths.cc.o' -MF 'src/25a6634@@mctree-mean-lengths@exe/tools_mctree-mean-lengths.cc.o.d' -o 'src/25a6634@@mctree-mean-lengths@exe/tools_mctree-mean-lengths.cc.o' -c ../src/tools/mctree-mean-lengths.cc
[200/256] c++ -o src/mctree-mean-lengths 'src/25a6634@@mctree-mean-lengths@exe/tools_mctree-mean-lengths.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[201/256] c++ -Isrc/25a6634@@trees-to-SRQ@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@trees-to-SRQ@exe/tools_trees-to-SRQ.cc.o' -MF 'src/25a6634@@trees-to-SRQ@exe/tools_trees-to-SRQ.cc.o.d' -o 'src/25a6634@@trees-to-SRQ@exe/tools_trees-to-SRQ.cc.o' -c ../src/tools/trees-to-SRQ.cc
[202/256] c++ -o src/trees-to-SRQ 'src/25a6634@@trees-to-SRQ@exe/tools_trees-to-SRQ.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[203/256] c++ -Isrc/25a6634@@pickout@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@pickout@exe/tools_pickout.cc.o' -MF 'src/25a6634@@pickout@exe/tools_pickout.cc.o.d' -o 'src/25a6634@@pickout@exe/tools_pickout.cc.o' -c ../src/tools/pickout.cc
[204/256] c++ -o src/pickout 'src/25a6634@@pickout@exe/tools_pickout.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[205/256] c++ -Isrc/25a6634@@cut-range@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@cut-range@exe/tools_cut-range.cc.o' -MF 'src/25a6634@@cut-range@exe/tools_cut-range.cc.o.d' -o 'src/25a6634@@cut-range@exe/tools_cut-range.cc.o' -c ../src/tools/cut-range.cc
[206/256] c++ -o src/cut-range 'src/25a6634@@cut-range@exe/tools_cut-range.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[207/256] c++ -Isrc/25a6634@@trees-distances@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@trees-distances@exe/tools_trees-distances.cc.o' -MF 'src/25a6634@@trees-distances@exe/tools_trees-distances.cc.o.d' -o 'src/25a6634@@trees-distances@exe/tools_trees-distances.cc.o' -c ../src/tools/trees-distances.cc
[208/256] c++ -o src/trees-distances 'src/25a6634@@trees-distances@exe/tools_trees-distances.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[209/256] c++ -Isrc/25a6634@@alignment-thin@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-thin@exe/tools_alignment-thin.cc.o' -MF 'src/25a6634@@alignment-thin@exe/tools_alignment-thin.cc.o.d' -o 'src/25a6634@@alignment-thin@exe/tools_alignment-thin.cc.o' -c ../src/tools/alignment-thin.cc
[210/256] c++ -o src/alignment-thin 'src/25a6634@@alignment-thin@exe/tools_alignment-thin.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[211/256] c++ -Isrc/25a6634@@alignments-diff@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignments-diff@exe/tools_alignments-diff.cc.o' -MF 'src/25a6634@@alignments-diff@exe/tools_alignments-diff.cc.o.d' -o 'src/25a6634@@alignments-diff@exe/tools_alignments-diff.cc.o' -c ../src/tools/alignments-diff.cc
[212/256] c++ -o src/alignments-diff 'src/25a6634@@alignments-diff@exe/tools_alignments-diff.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[213/256] c++ -Isrc/25a6634@@tree-tool@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@tree-tool@exe/tools_tree-tool.cc.o' -MF 'src/25a6634@@tree-tool@exe/tools_tree-tool.cc.o.d' -o 'src/25a6634@@tree-tool@exe/tools_tree-tool.cc.o' -c ../src/tools/tree-tool.cc
[214/256] c++ -Isrc/25a6634@@alignment-draw@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-draw@exe/tools_colors.cc.o' -MF 'src/25a6634@@alignment-draw@exe/tools_colors.cc.o.d' -o 'src/25a6634@@alignment-draw@exe/tools_colors.cc.o' -c ../src/tools/colors.cc
[215/256] c++ -o src/tree-tool 'src/25a6634@@tree-tool@exe/tools_tree-tool.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[216/256] c++ -Isrc/25a6634@@trees-bootstrap@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@trees-bootstrap@exe/tools_bootstrap.cc.o' -MF 'src/25a6634@@trees-bootstrap@exe/tools_bootstrap.cc.o.d' -o 'src/25a6634@@trees-bootstrap@exe/tools_bootstrap.cc.o' -c ../src/tools/bootstrap.cc
[217/256] c++ -Isrc/25a6634@@bali-subsample@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@bali-subsample@exe/tools_subsample.cc.o' -MF 'src/25a6634@@bali-subsample@exe/tools_subsample.cc.o.d' -o 'src/25a6634@@bali-subsample@exe/tools_subsample.cc.o' -c ../src/tools/subsample.cc
[218/256] c++ -o src/bali-subsample 'src/25a6634@@bali-subsample@exe/tools_subsample.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[219/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_fa55707295bf5660f1f349161980433307be4a61.dat
[220/256] c++ -Isrc/25a6634@@alignment-distances@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-distances@exe/tools_alignment-distances.cc.o' -MF 'src/25a6634@@alignment-distances@exe/tools_alignment-distances.cc.o.d' -o 'src/25a6634@@alignment-distances@exe/tools_alignment-distances.cc.o' -c ../src/tools/alignment-distances.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/tools/alignment-distances.cc:23:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘int main(int, char**)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[221/256] c++ -o src/alignment-distances 'src/25a6634@@alignment-distances@exe/tools_alignment-distances.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/:XXXXXXXXXXXXXXXX' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[222/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_e447c8fa22b6382913d068ab317fdac4d8663623.dat
[223/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_8a52ae461fd79a57888a1382db5e918353a8291b.dat
[224/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_015abfcb2cef030f1379dd9b32dfe28325c0a1bd.dat
[225/256] c++ -Isrc/25a6634@@alignment-draw@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@alignment-draw@exe/tools_alignment-draw.cc.o' -MF 'src/25a6634@@alignment-draw@exe/tools_alignment-draw.cc.o.d' -o 'src/25a6634@@alignment-draw@exe/tools_alignment-draw.cc.o' -c ../src/tools/alignment-draw.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/tree/tree.H:31,
from ../src/tools/alignment-draw.cc:23:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘std::vector<T> split(const string&, char) [with T = double]’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
[226/256] c++ -o src/alignment-draw 'src/25a6634@@alignment-draw@exe/tools_alignment-draw.cc.o' 'src/25a6634@@alignment-draw@exe/tools_colors.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[227/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_d525c722d9dbebbabac1b00db8568f71d06ac8ab.dat
[228/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_68d72c5cdfc97c68bd6bf3b89448cfab16c576d4.dat
[229/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_82abccb4b6463f2f47593d74425e5971302076f2.dat
[230/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_3296d17055a668d70f49fb9882768bb4576dc46a.dat
[231/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_b10d3a100fe0631a26ad65f108d522eee00338b3.dat
[232/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_e7af9cd439b7ee97f88465d93f1a7cb49dde3d57.dat
[233/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_5d96d6d303c70bc32b3259e8ac25fa30d3230b53.dat
[234/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_0fb329d6979c06fef2a4ef5a730e44bf523c4b89.dat
[235/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_65b0f65ada3f1d341e4395430f790c9349f9a933.dat
[236/256] c++ -Isrc/25a6634@@trees-bootstrap@exe -Isrc -I../src -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@trees-bootstrap@exe/tools_trees-bootstrap.cc.o' -MF 'src/25a6634@@trees-bootstrap@exe/tools_trees-bootstrap.cc.o.d' -o 'src/25a6634@@trees-bootstrap@exe/tools_trees-bootstrap.cc.o' -c ../src/tools/trees-bootstrap.cc
In file included from /usr/include/c++/8/bits/stl_algo.h:61,
from /usr/include/c++/8/algorithm:62,
from ../src/tools/trees-bootstrap.cc:35:
/usr/include/c++/8/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++/8/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
__adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
^~~~~~~~~~~~~
In file included from /usr/include/c++/8/algorithm:62,
from ../src/tools/trees-bootstrap.cc:35:
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’:
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
__insertion_sort(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1840:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h: In function ‘void std::__introsort_loop(_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++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
__introsort_loop(_RandomAccessIterator __first,
^~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1940:5: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
/usr/include/c++/8/bits/stl_algo.h:1954:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__cut, __last, __depth_limit, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h: In function ‘double greater_than(const std::valarray<double>&, std::valarray<double>, double)’:
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1968:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__introsort_loop(__first, __last,
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
std::__lg(__last - __first) * 2,
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
__comp);
~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1885:25: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_algo.h:1890:23: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
std::__insertion_sort(__first, __last, __comp);
~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
[237/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_47c63926356ee8c03fb0d4fadfbf662665e33e16.dat
[238/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_d8831729d19d78e24756b21c869ea264bfa18f39.dat
[239/256] c++ -o src/trees-bootstrap 'src/25a6634@@trees-bootstrap@exe/tools_trees-bootstrap.cc.o' 'src/25a6634@@trees-bootstrap@exe/tools_bootstrap.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
[240/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_83700cf4192d37877d2ad754aba2e7fe2b1d9d1c.dat
[241/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_03a4e0988bdae6a7e447207a701fe0caaf9d2b1b.dat
[242/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_58862dbcd443adc07b16898ff63f78cc8667a3c4.dat
[243/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_756906dfcf6eec1e3f535080ebba5aa2ce10bb55.dat
[244/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_7f459fd12208e9f73bebe4adc81ac956f6244f21.dat
[245/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_80163049db5939615519f334a546ba3aa887e4c8.dat
[246/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_b790d3ee8394b6ed5927e89e096e114047ce5eda.dat
[247/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_ea614a17be290010b65df455ded69e62c541d99f.dat
[248/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_3f6b47584c3b6569e4388927fecda914d14830ad.dat
[249/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_d4224fbcda9eb53540421f2b399900c0ca6c3fef.dat
[250/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_87d30c815d47ba48893be6e553c33fbe7371bbff.dat
[251/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_96fa5692d7e02cba4b7e4009929cfd9303ae5298.dat
[252/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_623d1911e3380c0038536f81acd8fa1b57fbd540.dat
[253/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_1873983c6be91ad29709a988809aec80c5542411.dat
[254/256] /usr/bin/meson --internal exe /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-private/meson_exe_pandoc_29d7b236a0463d15e413919b5db2463b4ffceb09.dat
[255/256] c++ -Isrc/25a6634@@draw-tree@exe -Isrc -I../src -I. -I../ -I/usr/include/cairo -I/usr/include/glib-2.0 -I/usr/lib/arm-linux-gnueabihf/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -fdiagnostics-color=always -pipe -D_FILE_OFFSET_BITS=64 -std=c++14 -DHAVE_CONFIG_H -Wall -Wextra -Wno-sign-compare -Woverloaded-virtual -Wstrict-aliasing -Wno-unknown-pragmas -Wno-maybe-uninitialized -DNDEBUG -DNDEBUG_DP -O3 -funroll-loops -ffast-math -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wdate-time -D_FORTIFY_SOURCE=2 -MD -MQ 'src/25a6634@@draw-tree@exe/tools_draw-tree.cc.o' -MF 'src/25a6634@@draw-tree@exe/tools_draw-tree.cc.o.d' -o 'src/25a6634@@draw-tree@exe/tools_draw-tree.cc.o' -c ../src/tools/draw-tree.cc
In file included from /usr/include/c++/8/vector:69,
from ../src/tools/draw-tree.cc:23:
/usr/include/c++/8/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++/8/bits/vector.tcc:413:7: 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
vector<_Tp, _Alloc>::
^~~~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {circular_range}; _Tp = circular_range; _Alloc = std::allocator<circular_range>]’:
/usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type ‘std::vector<circular_range>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<circular_range*, std::vector<circular_range> >’} changed in GCC 7.1
/usr/include/c++/8/bits/vector.tcc: In function ‘void equalize_daylight(tree_layout&, int)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<circular_range*, std::vector<circular_range> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘void equalize_daylight_greedy(tree_layout&, int)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<circular_range*, std::vector<circular_range> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/vector.tcc: In function ‘bool subtrees_of_node_overlap(tree_layout&, int)’:
/usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<circular_range*, std::vector<circular_range> >’ changed in GCC 7.1
_M_realloc_insert(end(), std::forward<_Args>(__args)...);
^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/8/vector:64,
from ../src/tools/draw-tree.cc:23:
/usr/include/c++/8/bits/stl_vector.h: In member function ‘virtual double energy2::operator()(const graph_layout&, std::vector<point_position>&) const’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h: In function ‘MC_tree_with_lengths get_MC_tree_with_lengths(const string&)’:
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
/usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
_M_realloc_insert(end(), __x);
^~~~~~~~~~~~~~~~~
[256/256] c++ -o src/draw-tree 'src/25a6634@@draw-tree@exe/tools_draw-tree.cc.o' -Wl,--no-undefined -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0 -Wl,-z,relro -Wl,-z,now -Wl,--start-group src/libbali-phy.a -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono /usr/lib/arm-linux-gnueabihf/libcairo.so -lboost_program_options -lboost_random -lboost_system -lboost_filesystem -lboost_chrono -Wl,--end-group '-Wl,-rpath,$ORIGIN/' -Wl,-rpath-link,/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src
dh_auto_test -a -O--buildsystem=meson
cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 ninja test
[1/4] Generating git-version.h with a custom command.
[1/2] Running all tests.
1/30 bali-phy version OK 0.04 s
2/30 bali-phy help OK 0.04 s
3/30 bali-phy 5d test OK 3.70 s
4/30 bali-phy 5d +A 50 OK 18.49 s
5/30 bali-phy 5d -A 200 FAIL 5.89 s (exit status 1)
6/30 model_P --help OK 0.01 s
7/30 statreport --help OK 0.01 s
8/30 stats-select --help OK 0.01 s
9/30 alignment-gild --help OK 0.01 s
10/30 alignment-consensus --help OK 0.01 s
11/30 alignment-max --help OK 0.01 s
12/30 alignment-chop-internal --help OK 0.01 s
13/30 alignment-indices --help OK 0.01 s
14/30 alignment-info --help OK 0.01 s
15/30 alignment-cat --help OK 0.01 s
16/30 alignment-translate --help OK 0.01 s
17/30 alignment-find --help OK 0.01 s
18/30 trees-consensus --help OK 0.01 s
19/30 tree-mean-lengths --help OK 0.01 s
20/30 mctree-mean-lengths --help OK 0.01 s
21/30 trees-to-SRQ --help OK 0.01 s
22/30 pickout --help OK 0.01 s
23/30 cut-range --help OK 0.01 s
24/30 trees-distances --help OK 0.01 s
25/30 alignment-thin --help OK 0.01 s
26/30 alignments-diff --help OK 0.01 s
27/30 tree-tool --help OK 0.01 s
28/30 alignment-distances --help OK 0.01 s
29/30 subsample --help OK 0.01 s
30/30 bali-phy testsuite OK 284.67 s
Ok: 29
Expected Fail: 0
Fail: 1
Unexpected Pass: 0
Skipped: 0
Timeout: 0
The output from the failed tests:
5/30 bali-phy 5d -A 200 FAIL 5.89 s (exit status 1)
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta --iter=200 --package-path=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/builtins:/<<BUILDDIR>>/bali-phy-3.4.1+dfsg -Inone
--- stdout ---
T:topology ~ uniform on tree topologies
T:lengths ~ iid[num_branches[T],gamma[0.5,div[2,num_branches[T]]]]
Partition [1;35mP1[0m:
file = [1m[1m/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta[0m[0m
alphabet = [1mDNA[0m
subst = [1mtn93[0m ([1;34mS1[0m)
indel = [1mnone[0m
scale ~ [1mgamma[0.5,2][0m ([0;32mScale1[0m)
Substitution model [1;34mS1[0m priors:
tn93:kappaPur ~ log_normal[log[2],0.25]
tn93:kappaPyr ~ log_normal[log[2],0.25]
tn93:pi ~ dirichlet_on[letters[@a],1]
Beginning pre-burnin: 3 iterations.
Start #1 prior = 4.09869 likelihood = -1545.24 |T| = 0.836783 |A| = 110 Scale1*|T| = 0.259527
Tree (S)ize #1 prior = -38.8482 likelihood = -966.813 |T| = 0.836783 |A| = 110 Scale1*|T| = 67.4809
Tree (S)ize #2 prior = -33.5957 likelihood = -968.949 |T| = 0.854461 |A| = 110 Scale1*|T| = 59.8204
Tree (S)ize #3 prior = -21.7432 likelihood = -968.602 |T| = 1.6608 |A| = 110 Scale1*|T| = 60.877
(S)+Branch (L)engths #1 prior = -24.0157 likelihood = -963.776 |T| = 2.70625 |A| = 110 Scale1*|T| = 81.9233
(S)+Branch (L)engths #2 prior = -4.55046 likelihood = -940.697 |T| = 1.9629 |A| = 110 Scale1*|T| = 4.65117
(S)+Branch (L)engths #3 prior = -3.91129 likelihood = -916.617 |T| = 1.41283 |A| = 110 Scale1*|T| = 4.03474
(S)+(L)+(P)arameters #1 prior = -6.99838 likelihood = -799.527 |T| = 2.13837 |A| = 110 Scale1*|T| = 6.21116
(S)+(L)+(P)arameters #2 prior = -14.2963 likelihood = -788.676 |T| = 3.70826 |A| = 110 Scale1*|T| = 12.0596
(S)+(L)+(P)arameters #3 prior = -6.19122 likelihood = -789.769 |T| = 1.81254 |A| = 110 Scale1*|T| = 8.07045
(S)+(L)+(P)+NNI #1 prior = -7.23953 likelihood = -790.854 |T| = 2.09887 |A| = 110 Scale1*|T| = 8.01062
(S)+(L)+(P)+NNI #2 prior = -3.98477 likelihood = -793.926 |T| = 1.93292 |A| = 110 Scale1*|T| = 9.62085
(S)+(L)+(P)+NNI #3 prior = -5.10952 likelihood = -793.386 |T| = 1.94068 |A| = 110 Scale1*|T| = 9.93006
(S)+(L)+(P)+NNI #4 prior = -4.62476 likelihood = -791.111 |T| = 2.27866 |A| = 110 Scale1*|T| = 10.214
SPR #1 prior = -5.40496 likelihood = -790.688 |T| = 1.44127 |A| = 110 Scale1*|T| = 7.43854
(S)+(L)+(P)+NNI #1 prior = -3.882 likelihood = -789.668 |T| = 0.860797 |A| = 110 Scale1*|T| = 6.20784
(S)+(L)+(P)+NNI #2 prior = -1.88822 likelihood = -794.679 |T| = 0.793484 |A| = 110 Scale1*|T| = 4.268
(S)+(L)+(P)+NNI #3 prior = -2.34613 likelihood = -791.78 |T| = 0.652903 |A| = 110 Scale1*|T| = 5.16442
Finished pre-burnin in 0.28 seconds.
BAli-Phy does NOT detect how many iterations is sufficient:
You need to monitor convergence and kill it when done.
Maximum number of iterations set to 200.
Beginning MCMC computations.
- Future screen output sent to '5d-1/C1.out'
- Future debugging output sent to '5d-1/C1.err'
- Sampled trees logged to '5d-1/C1.trees'
- Sampled alignments logged to '5d-1/C1.P<partition>.fastas'
- Run info written to '5d-1/C1.run.json'
- Sampled numerical parameters logged to '5d-1/C1.log'
You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical).
See the manual at http://www.bali-phy.org/README.xhtml for further information.
--- stderr ---
Home directory '/sbuild-nonexistent' does not exist!
Partition #1: 126 columns -> 110 unique patterns.
Created directory '5d-1/' for output files.
bali-phy: Error! move = sampler
submove = tree
move = tree
submove = topology
move = topology
submove = SPR
move = SPR
submove = SPR_all
[single] move = SPR_all
bool sample_SPR_search_one(Parameters&, MCMC::MoveStats&, const tree_edge&, const spr_range&, bool)int choose_MH(int, const std::vector<T>&) [with F = log_double_t]:
No option chosen! (current = 0)
*log(Pr[0]) = nan
log(Pr[1]) = nan
log(Pr[2]) = nan
log(Pr[3]) = nan
log(Pr[4]) = nan
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN16choose_exceptionI12log_double_tEC2EiRKSt6vectorIS0_SaIS0_EE+0xef8) [0x14c53c]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z9choose_MHI12log_double_tEiiRKSt6vectorIT_SaIS2_EE+0xc8c) [0x1961b4]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z21sample_SPR_search_oneR10ParametersRN4MCMC9MoveStatsERK9tree_edgeRKSt3mapIS4_bSt4lessIS4_ESaISt4pairIS5_bEEEb+0x69c) [0x1ed1c4]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z21sample_SPR_search_oneR10ParametersRN4MCMC9MoveStatsERK9tree_edgeb+0x54) [0x1ee214]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z14sample_SPR_allR9owned_ptrI5ModelERN4MCMC9MoveStatsE+0xac) [0x1ef390]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC10SingleMove7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x50) [0x13fabc]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x64) [0x13f900]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x64) [0x13f900]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x64) [0x13f900]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x64) [0x13f900]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC7Sampler2goER9owned_ptrI5ModelEiiRSo+0x534) [0x143bf8]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z11do_samplingRKN5boost15program_options13variables_mapER9owned_ptrI5ModelElRSoRKSt6vectorISt8functionIFvRKS5_lEESaISE_EE+0xc44) [0x24bac0]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(main+0x23cc) [0xaa98c]
/lib/arm-linux-gnueabihf/libc.so.6(__libc_start_main+0x10c) [0xf6eb7718]
-------
Full log written to /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/meson-logs/testlog.txt
FAILED: meson-test
/usr/bin/meson test --no-rebuild --print-errorlogs
ninja: build stopped: subcommand failed.
cd obj-arm-linux-gnueabihf && tail -v -n \+0 meson-logs/testlog.txt
==> meson-logs/testlog.txt <==
Log of Meson test suite run on 2019-07-10T05:50:21.816768
Inherited environment: DEB_HOST_GNU_SYSTEM='linux-gnueabihf' DEB_TARGET_GNU_CPU='arm' DEB_BUILD_ARCH_BITS='32' DEB_HOST_ARCH_OS='linux' USER='buildd' CXXFLAGS='-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0' DEB_TARGET_MULTIARCH='arm-linux-gnueabihf' DEB_BUILD_GNU_TYPE='arm-linux-gnueabihf' OBJCFLAGS='-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' DEB_HOST_ARCH_ABI='eabihf' DEB_BUILD_ARCH_CPU='arm' DEB_HOST_ARCH_LIBC='gnu' HOME='/sbuild-nonexistent' APT_CONFIG='/var/lib/sbuild/apt.conf' SCHROOT_CHROOT_NAME='bullseye-staging-armhf-sbuild' DEB_BUILD_ARCH_ENDIAN='little' LDFLAGS='-Wl,-z,relro -Wl,-z,now' DEB_TARGET_ARCH_BITS='32' SCHROOT_UID='107' MAKEFLAGS='' DEB_BUILD_GNU_SYSTEM='linux-gnueabihf' DEB_BUILD_ARCH_OS='linux' DEB_TARGET_GNU_TYPE='arm-linux-gnueabihf' DEB_TARGET_ARCH_CPU='arm' LOGNAME='buildd' DEB_BUILD_ARCH_LIBC='gnu' DEB_BUILD_ARCH_ABI='eabihf' DEB_CFLAGS_MAINT_APPEND='-O3 -g0' DEB_TARGET_ARCH_ENDIAN='little' DEB_HOST_ARCH='armhf' DEB_TARGET_GNU_SYSTEM='linux-gnueabihf' DEB_HOST_GNU_CPU='arm' PATH='/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' MESON_TESTTHREADS='4' DEB_TARGET_ARCH_OS='linux' MAKELEVEL='1' CFLAGS='-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -g0' SCHROOT_COMMAND='dpkg-buildpackage -us -uc -mRaspbian mythic lxc autobuilder 1 <root@raspbian.org> -B -rfakeroot' SOURCE_DATE_EPOCH='1562571091' SCHROOT_SESSION_ID='bullseye-staging-armhf-sbuild-f130a75c-b13a-4a18-9951-e9edeaa7167f' DEB_HOST_MULTIARCH='arm-linux-gnueabihf' FCFLAGS='-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong' SCHROOT_ALIAS_NAME='bullseye-staging-armhf-sbuild' OBJCXXFLAGS='-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security' DEB_TARGET_ARCH_ABI='eabihf' DEB_TARGET_ARCH_LIBC='gnu' SCHROOT_USER='buildd' DEB_BUILD_OPTIONS='parallel=4' SCHROOT_GROUP='buildd' DH_INTERNAL_BUILDFLAGS='1' CPPFLAGS='-Wdate-time -D_FORTIFY_SOURCE=2' SHELL='/bin/sh' DEB_HOST_ARCH_BITS='32' DEB_BUILD_ARCH='armhf' DEB_BUILD_MAINT_OPTIONS='hardening=+all' DEB_BUILD_GNU_CPU='arm' DEB_HOST_GNU_TYPE='arm-linux-gnueabihf' DEB_HOST_ARCH_CPU='arm' DEB_RULES_REQUIRES_ROOT='binary-targets' LC_ALL='C.UTF-8' PWD='/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf' DEB_BUILD_MULTIARCH='arm-linux-gnueabihf' FFLAGS='-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong' SCHROOT_GID='112' MFLAGS='' GCJFLAGS='-g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg=. -fstack-protector-strong' DEB_CXXFLAGS_MAINT_APPEND='-O3 -g0' DEB_HOST_ARCH_ENDIAN='little' DEB_TARGET_ARCH='armhf'
1/30 bali-phy version OK 0.04 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy --version
--- stdout ---
VERSION: 3.4.1
BUILD: Jul 8 2019 07:31:31
ARCH: linux arm
COMPILER: gcc 8.3.0 arm
-------
2/30 bali-phy help OK 0.04 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy --help
--- stdout ---
Bayesian Inference of Alignment and Phylogeny
Usage: bali-phy <sequence-file1> [<sequence-file2> ...] [OPTIONS]
[1mBasic[0m options:
General options:
-h [ --help ] [=arg(=basic)] Print usage information.
-v [ --version ] Print version information.
-t [ --test ] Analyze the initial values and exit.
MCMC options:
-i [ --iterations ] arg The number of iterations to run.
-n [ --name ] arg Name for the output directory to create.
Parameter options:
--align arg Sequence file & initial alignment.
-T [ --tree ] arg File with initial tree
Model options:
-A [ --alphabet ] arg The alphabet.
-S [ --smodel ] arg Substitution model.
-I [ --imodel ] arg Insertion-deletion model.
-R [ --scale ] arg Prior on the scale.
-L [ --link ] arg Link partitions.
Showing [1mbasic[0m command line options. Not all options are shown!
* See `bali-phy help [1madvanced[0m` to see more options.
See `bali-phy help [4moption[24m` for help on [4moption[24m. For example,
* `bali-phy help [1malphabet[0m` shows help on the [1m--alphabet[0m command.
* `bali-phy help [1mimodel[0m` shows help on the [1m--imodel[0m command.
See `bali-phy help [4mfunction[24m` for help on [4mfunction[24m. For example,
* `bali-phy help [1mnormal[0m` shows help on the normal distribution.
* `bali-phy help [1mtn93[0m` shows help on the TN93 model.
* `bali-phy help [1mlog[0m` shows help on the log function.
* `bali-phy help [1mfunctions[0m` lists all the functions.
See `bali-phy help [1mtopics[0m` for an overview of help topics.
-------
3/30 bali-phy 5d test OK 3.70 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta --test --package-path=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/builtins:/<<BUILDDIR>>/bali-phy-3.4.1+dfsg
--- stdout ---
T:topology ~ uniform on tree topologies
T:lengths ~ iid[num_branches[T],gamma[0.5,div[2,num_branches[T]]]]
Partition [1;35mP1[0m:
file = [1m[1m/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta[0m[0m
alphabet = [1mDNA[0m
subst = [1mtn93[0m ([1;34mS1[0m)
indel = [1mrs07[0m ([1;31mI1[0m)
scale ~ [1mgamma[0.5,2][0m ([0;32mScale1[0m)
Substitution model [1;34mS1[0m priors:
tn93:kappaPur ~ log_normal[log[2],0.25]
tn93:kappaPyr ~ log_normal[log[2],0.25]
tn93:pi ~ dirichlet_on[letters[@a],1]
Insertion/deletion model [1;31mI1[0m priors:
rs07:log_rate ~ laplace[-4,0.707]
rs07:mean_length ~ exponential[10,1]
iter = 0 prior = -35.670774996433053 likelihood = -1498.661840692265514 posterior = -1534.332615688698525 prior_A = -35.311086090908347 |A| = 126 #indels = 4 |indels| = 12 #substs = 262 P1/likelihood = -1498.661840692265514 P1/prior_A = -35.311086090908347 P1/|A| = 126 P1/#indels = 4 P1/|indels| = 12 P1/#substs = 262 Scale[1]*|T| = 0.386139440000627 |T| = 0.830618426477639 Heat.beta = 1.000000000000000 Scale[1] = 0.464881861143039 rs07:mean_length = 10.348210695494268 rs07:log_rate = -3.766082856725239 tn93:pi[A] = 0.350699165622301 tn93:pi[C] = 0.549461746786763 tn93:pi[G] = 0.009076734460776 tn93:pi[T] = 0.090762353130161 tn93:kappaPyr = 2.176134430312400 tn93:kappaPur = 1.908666600855939
start time: Wed Jul 10 05:50:21 2019
end time: Wed Jul 10 05:50:25 2019
total (elapsed) time: 3 seconds
total (CPU) time: 3 seconds
--- stderr ---
Home directory '/sbuild-nonexistent' does not exist!
-------
4/30 bali-phy 5d +A 50 OK 18.49 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta --iter=50 --package-path=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/builtins:/<<BUILDDIR>>/bali-phy-3.4.1+dfsg
--- stdout ---
T:topology ~ uniform on tree topologies
T:lengths ~ iid[num_branches[T],gamma[0.5,div[2,num_branches[T]]]]
Partition [1;35mP1[0m:
file = [1m[1m/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta[0m[0m
alphabet = [1mDNA[0m
subst = [1mtn93[0m ([1;34mS1[0m)
indel = [1mrs07[0m ([1;31mI1[0m)
scale ~ [1mgamma[0.5,2][0m ([0;32mScale1[0m)
Substitution model [1;34mS1[0m priors:
tn93:kappaPur ~ log_normal[log[2],0.25]
tn93:kappaPyr ~ log_normal[log[2],0.25]
tn93:pi ~ dirichlet_on[letters[@a],1]
Insertion/deletion model [1;31mI1[0m priors:
rs07:log_rate ~ laplace[-4,0.707]
rs07:mean_length ~ exponential[10,1]
Beginning pre-burnin: 3 iterations.
Start #1 prior = -35.5392 likelihood = -1773.3 |T| = 0.894735 |A| = 126 Scale1*|T| = 0.156138
Tree (S)ize #1 prior = -24.9036 likelihood = -1068.82 |T| = 0.894735 |A| = 126 Scale1*|T| = 48.6779
Tree (S)ize #2 prior = -14.8778 likelihood = -1072.2 |T| = 1.00223 |A| = 126 Scale1*|T| = 33.3719
Tree (S)ize #3 prior = -14.2376 likelihood = -1069.62 |T| = 2.14953 |A| = 126 Scale1*|T| = 41.262
(S)+Branch (L)engths #1 prior = -17.6311 likelihood = -1068.53 |T| = 2.12856 |A| = 126 Scale1*|T| = 48.2243
(S)+Branch (L)engths #2 prior = -4.95925 likelihood = -1041.12 |T| = 0.881398 |A| = 126 Scale1*|T| = 9.42592
(S)+Branch (L)engths #3 prior = -2.44358 likelihood = -1017.02 |T| = 0.702663 |A| = 126 Scale1*|T| = 4.38318
(S)+(L)+(P)arameters #1 prior = -7.1523 likelihood = -877.8 |T| = 1.74647 |A| = 126 Scale1*|T| = 3.72692
(S)+(L)+(P)arameters #2 prior = -4.55388 likelihood = -813.062 |T| = 0.728619 |A| = 126 Scale1*|T| = 7.30181
(S)+(L)+(P)arameters #3 prior = -11.3044 likelihood = -792.342 |T| = 2.12512 |A| = 126 Scale1*|T| = 7.63942
(S)+(L)+(P)+NNI #1 prior = -14.1365 likelihood = -793.314 |T| = 2.33543 |A| = 126 Scale1*|T| = 6.13016
(S)+(L)+(P)+NNI #2 prior = -7.21327 likelihood = -794.948 |T| = 0.703845 |A| = 126 Scale1*|T| = 6.16393
(S)+(L)+(P)+NNI #3 prior = -6.99479 likelihood = -792.611 |T| = 1.59115 |A| = 126 Scale1*|T| = 7.03238
(S)+(L)+(P)+NNI #4 prior = -3.47353 likelihood = -793.749 |T| = 0.871795 |A| = 126 Scale1*|T| = 7.44558
SPR #1 prior = -4.92989 likelihood = -791.299 |T| = 1.07521 |A| = 126 Scale1*|T| = 8.23053
(S)+(L)+(P)+NNI #1 prior = -10.3146 likelihood = -792.679 |T| = 1.70824 |A| = 126 Scale1*|T| = 6.05082
(S)+(L)+(P)+NNI #2 prior = -8.97747 likelihood = -791.328 |T| = 0.993501 |A| = 126 Scale1*|T| = 7.64571
(S)+(L)+(P)+NNI #3 prior = -5.29343 likelihood = -792.04 |T| = 0.862444 |A| = 126 Scale1*|T| = 8.37523
Finished pre-burnin in 0.3 seconds.
BAli-Phy does NOT detect how many iterations is sufficient:
You need to monitor convergence and kill it when done.
Maximum number of iterations set to 50.
Beginning MCMC computations.
- Future screen output sent to '5d-2/C1.out'
- Future debugging output sent to '5d-2/C1.err'
- Sampled trees logged to '5d-2/C1.trees'
- Sampled alignments logged to '5d-2/C1.P<partition>.fastas'
- Run info written to '5d-2/C1.run.json'
- Sampled numerical parameters logged to '5d-2/C1.log'
You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical).
See the manual at http://www.bali-phy.org/README.xhtml for further information.
--- stderr ---
Home directory '/sbuild-nonexistent' does not exist!
Created directory '5d-2/' for output files.
-------
5/30 bali-phy 5d -A 200 FAIL 5.89 s (exit status 1)
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta --iter=200 --package-path=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/builtins:/<<BUILDDIR>>/bali-phy-3.4.1+dfsg -Inone
--- stdout ---
T:topology ~ uniform on tree topologies
T:lengths ~ iid[num_branches[T],gamma[0.5,div[2,num_branches[T]]]]
Partition [1;35mP1[0m:
file = [1m[1m/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/../examples/sequences/5S-rRNA/5d.fasta[0m[0m
alphabet = [1mDNA[0m
subst = [1mtn93[0m ([1;34mS1[0m)
indel = [1mnone[0m
scale ~ [1mgamma[0.5,2][0m ([0;32mScale1[0m)
Substitution model [1;34mS1[0m priors:
tn93:kappaPur ~ log_normal[log[2],0.25]
tn93:kappaPyr ~ log_normal[log[2],0.25]
tn93:pi ~ dirichlet_on[letters[@a],1]
Beginning pre-burnin: 3 iterations.
Start #1 prior = 4.09869 likelihood = -1545.24 |T| = 0.836783 |A| = 110 Scale1*|T| = 0.259527
Tree (S)ize #1 prior = -38.8482 likelihood = -966.813 |T| = 0.836783 |A| = 110 Scale1*|T| = 67.4809
Tree (S)ize #2 prior = -33.5957 likelihood = -968.949 |T| = 0.854461 |A| = 110 Scale1*|T| = 59.8204
Tree (S)ize #3 prior = -21.7432 likelihood = -968.602 |T| = 1.6608 |A| = 110 Scale1*|T| = 60.877
(S)+Branch (L)engths #1 prior = -24.0157 likelihood = -963.776 |T| = 2.70625 |A| = 110 Scale1*|T| = 81.9233
(S)+Branch (L)engths #2 prior = -4.55046 likelihood = -940.697 |T| = 1.9629 |A| = 110 Scale1*|T| = 4.65117
(S)+Branch (L)engths #3 prior = -3.91129 likelihood = -916.617 |T| = 1.41283 |A| = 110 Scale1*|T| = 4.03474
(S)+(L)+(P)arameters #1 prior = -6.99838 likelihood = -799.527 |T| = 2.13837 |A| = 110 Scale1*|T| = 6.21116
(S)+(L)+(P)arameters #2 prior = -14.2963 likelihood = -788.676 |T| = 3.70826 |A| = 110 Scale1*|T| = 12.0596
(S)+(L)+(P)arameters #3 prior = -6.19122 likelihood = -789.769 |T| = 1.81254 |A| = 110 Scale1*|T| = 8.07045
(S)+(L)+(P)+NNI #1 prior = -7.23953 likelihood = -790.854 |T| = 2.09887 |A| = 110 Scale1*|T| = 8.01062
(S)+(L)+(P)+NNI #2 prior = -3.98477 likelihood = -793.926 |T| = 1.93292 |A| = 110 Scale1*|T| = 9.62085
(S)+(L)+(P)+NNI #3 prior = -5.10952 likelihood = -793.386 |T| = 1.94068 |A| = 110 Scale1*|T| = 9.93006
(S)+(L)+(P)+NNI #4 prior = -4.62476 likelihood = -791.111 |T| = 2.27866 |A| = 110 Scale1*|T| = 10.214
SPR #1 prior = -5.40496 likelihood = -790.688 |T| = 1.44127 |A| = 110 Scale1*|T| = 7.43854
(S)+(L)+(P)+NNI #1 prior = -3.882 likelihood = -789.668 |T| = 0.860797 |A| = 110 Scale1*|T| = 6.20784
(S)+(L)+(P)+NNI #2 prior = -1.88822 likelihood = -794.679 |T| = 0.793484 |A| = 110 Scale1*|T| = 4.268
(S)+(L)+(P)+NNI #3 prior = -2.34613 likelihood = -791.78 |T| = 0.652903 |A| = 110 Scale1*|T| = 5.16442
Finished pre-burnin in 0.28 seconds.
BAli-Phy does NOT detect how many iterations is sufficient:
You need to monitor convergence and kill it when done.
Maximum number of iterations set to 200.
Beginning MCMC computations.
- Future screen output sent to '5d-1/C1.out'
- Future debugging output sent to '5d-1/C1.err'
- Sampled trees logged to '5d-1/C1.trees'
- Sampled alignments logged to '5d-1/C1.P<partition>.fastas'
- Run info written to '5d-1/C1.run.json'
- Sampled numerical parameters logged to '5d-1/C1.log'
You can examine 'C1.log' using BAli-Phy tool statreport (command-line) or the BEAST program Tracer (graphical).
See the manual at http://www.bali-phy.org/README.xhtml for further information.
--- stderr ---
Home directory '/sbuild-nonexistent' does not exist!
Partition #1: 126 columns -> 110 unique patterns.
Created directory '5d-1/' for output files.
bali-phy: Error! move = sampler
submove = tree
move = tree
submove = topology
move = topology
submove = SPR
move = SPR
submove = SPR_all
[single] move = SPR_all
bool sample_SPR_search_one(Parameters&, MCMC::MoveStats&, const tree_edge&, const spr_range&, bool)int choose_MH(int, const std::vector<T>&) [with F = log_double_t]:
No option chosen! (current = 0)
*log(Pr[0]) = nan
log(Pr[1]) = nan
log(Pr[2]) = nan
log(Pr[3]) = nan
log(Pr[4]) = nan
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN16choose_exceptionI12log_double_tEC2EiRKSt6vectorIS0_SaIS0_EE+0xef8) [0x14c53c]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z9choose_MHI12log_double_tEiiRKSt6vectorIT_SaIS2_EE+0xc8c) [0x1961b4]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z21sample_SPR_search_oneR10ParametersRN4MCMC9MoveStatsERK9tree_edgeRKSt3mapIS4_bSt4lessIS4_ESaISt4pairIS5_bEEEb+0x69c) [0x1ed1c4]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z21sample_SPR_search_oneR10ParametersRN4MCMC9MoveStatsERK9tree_edgeb+0x54) [0x1ee214]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z14sample_SPR_allR9owned_ptrI5ModelERN4MCMC9MoveStatsE+0xac) [0x1ef390]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC10SingleMove7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x50) [0x13fabc]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x64) [0x13f900]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x64) [0x13f900]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x64) [0x13f900]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC9MoveGroup7iterateER9owned_ptrI5ModelERNS_9MoveStatsEi+0x64) [0x13f900]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_ZN4MCMC7Sampler2goER9owned_ptrI5ModelEiiRSo+0x534) [0x143bf8]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(_Z11do_samplingRKN5boost15program_options13variables_mapER9owned_ptrI5ModelElRSoRKSt6vectorISt8functionIFvRKS5_lEESaISE_EE+0xc44) [0x24bac0]
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy(main+0x23cc) [0xaa98c]
/lib/arm-linux-gnueabihf/libc.so.6(__libc_start_main+0x10c) [0xf6eb7718]
-------
6/30 model_P --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/model_P --help
--- stdout ---
Compute marginal likelihoods using stabilized harmonic mean estimator
Usage: model_P < in-file
Allowed options:
--help produce help message
--seed arg random seed
--verbose Output more log messages on stderr.
-------
7/30 statreport --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/statreport --help
--- stdout ---
Compute summary statistics for tab-delimited data files.
Usage: statreport [OPTIONS] file1 [file2 file3 ... ]
All options:
-h [ --help ] Produce help message.
--ignore arg Do not analyze these fields.
--select arg Analyze only these fields.
-i [ --individual ] Show results for individual files separately
also.
-s [ --skip ] arg (=10%) Number of initial lines to skip.
-x [ --subsample ] arg (=1) Factor by which to sub-sample.
--truth arg True value
--min arg Required minimum number of lines to read.
-u [ --until ] arg Read until this number of trees.
--mean Show mean and standard deviation.
--mode Show mode (with precision)
--log-mean Show log mean of X given log X.
--median Show median and confidence level.
--confidence arg (=0.95) Confidence interval levels (colon-separated).
--BCI arg (=HPD) Type of Bayesian Credible Interval (BCI): HPD or
central
-p [ --precision ] arg (=4) Number of significant figures.
-v [ --verbose ] Output more log messages on stderr.
Default: Report the median and 95% credible interval for each column.
-------
8/30 stats-select --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/stats-select --help
--- stdout ---
Select columns from a Tracer-format data file.
Usage: stats-select [OPTIONS] column-name [column-name ...] < data-file
All options:
--help Produce help message
--no-header Suppress the line of column names.
-s [ --select ] arg Select on key=value pairs
-r [ --remove ] Remove selected columns, instead of keeping them.
-a [ --add ] arg Remove selected columns, instead of keeping them.
-------
9/30 alignment-gild --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-gild --help
--- stdout ---
Annotate each residue in the alignment according to the probability that it should align to the hypothetical root character in its column.
Usage: alignment-gild alignment-file tree-file ... [OPTIONS] < alignments-file
Allowed options:
-h [ --help ] produce help message
--align arg file with sequences and initial alignment
--tree arg file with initial tree
--find-root estimate the root position from branch lengths
--alphabet arg set to 'Codons' to prefer codon alphabets
--skip arg (=0) number of alignment samples to skip
--max-alignments arg (=1000) maximum number of alignments to analyze
-v [ --verbose ] Output more log messages on stderr.
-------
10/30 alignment-consensus --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-consensus --help
--- stdout ---
Construct a consensus alignment to summarize an alignment sample.
Usage: alignment-consensus [OPTIONS] < alignments-file
Allowed options:
-h [ --help ] produce help message
--alphabet arg Specify the alphabet: DNA, RNA, Amino-Acids,
Amino-Acids+stop, Triplets, Codons, or
Codons+stop.
--seed arg random seed
--skip arg (=0) number of tree samples to skip
--max-alignments arg (=1000) maximum number of alignments to analyze
--strict arg ignore events below this probability
--cutoff arg ignore events below this probability
--uncertainty arg file-name for AU uncertainty vs level
--verbose Output more log messages on stderr.
-------
11/30 alignment-max --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-max --help
--- stdout ---
Construct a posterior decoding alignment to summarize an alignment sample.
Usage: alignment-max [OPTIONS] < alignments-file
Allowed options:
-h [ --help ] Produce help message
--alphabet arg Specify the alphabet: DNA, RNA,
Amino-Acids, Amino-Acids+stop, Triplets,
Codons, or Codons+stop.
-s [ --skip ] arg (=0) Number of alignment samples to skip
-m [ --max-alignments ] arg (=1000) Maximum number of alignments to analyze
--analysis arg (=wsum) sum, wsum, multiply
-o [ --out ] arg (=-) Output file (defaults to stdout)
-p [ --out-probabilities ] arg Output file for column probabilities, if
specified
-v [ --verbose ] Output more log messages on stderr.
-------
12/30 alignment-chop-internal --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-chop-internal --help
--- stdout ---
Remove ancestral sequences from an alignment.
Usage: alignment-chop-internal [OPTIONS] < <alignments-file>
Allowed options:
-h [ --help ] produce help message
--align arg file with sequences and initial alignment
--alphabet arg set to 'Codons' to prefer codon alphabets
--tree arg file with tree that specifies leaves to keep
-N [ --nleaves ] arg number of sequences to keep
-------
13/30 alignment-indices --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-indices --help
--- stdout ---
Show the alignment in terms of the index of each character in its sequence.
Usage: alignment-indices <alignment-file> [OPTIONS]
Allowed options:
-h [ --help ] produce help message
--align arg file with sequences and initial alignment
--alphabet arg set to 'Codons' to prefer codon alphabets
-c [ --columns ] arg Ranges of columns to keep, like: 1-10,30-
--invariant arg print only sites where this site and <arg> neighbors
are invariant.
--differences arg how many sequences may differ from the majority?
--avoid-gaps arg (=3) How far from a gap must a column be to be invariant?
--min-constraints arg Minimum # of constraints per column for a constraint to
be emitted
-------
14/30 alignment-info --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-info --help
--- stdout ---
Show useful statistics about the alignment.
Usage: alignment-info <alignment-file> [<tree-file>] [OPTIONS]
Allowed options:
--help produce help message
--align arg file with sequences and initial alignment
--tree arg file with initial tree
--alphabet arg specify the alphabet: DNA, RNA, Amino-Acids, Triplets,
or Codons
-------
15/30 alignment-cat --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-cat --help
--- stdout ---
Concatenate several alignments (with the same sequence names) end-to-end.
Usage: alignment-cat <file1> [<file2> ...]
All options:
-h [ --help ] Produce help message
--output arg (=fasta) Which output format: fasta or phylip?
-c [ --columns ] arg Ranges of columns to keep, like: 1-10,30-
-t [ --taxa ] arg Taxa to keep, comma-separated
-p [ --pad ] Add gaps to make sequence lengths identical
-r [ --reverse ] Reverse the sequences
-e [ --erase-empty-columns ] Remove columns with no characters (all gaps).
--missing arg (=-?) What letters are not characters (e.g. gaps)?
--strip-gaps Remove all non-character letters from
sequences.
--reorder-by-tree arg Reorder the sequences given a tree
--use-root use the root specified in the tree file to
reorder
--reorder-by-alignment arg Reorder the sequences following an alignment
--align-by-amino arg Arrange nucleotides into codon alignment
Examples:
To select columns from an alignment:
% alignment-cat -c1-10,50-100,600- filename.fasta > result.fasta
% alignment-cat -c5-250/3 filename.fasta > first_codon_position.fasta
% alignment-cat -c6-250/3 filename.fasta > second_codon_position.fasta
To concatenate two or more alignments:
% alignment-cat filename1.fasta filename2.fasta > all.fasta
-------
16/30 alignment-translate --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-translate --help
--- stdout ---
Translate a DNA/RNA alignment into amino acids.
Usage: alignment-translate [OPTIONS] < sequence-file [OPTIONS]
Allowed options:
-h [ --help ] Produce help message
-g [ --genetic-code ] arg (=standard) Specify alternate genetic code.
-f [ --frame ] arg (=1) Frame 1, 2, 3, -1, -2, or -3
-r [ --reverse ] Just return the reverse
-c [ --complement ] Just return the complement
-t [ --translate ] arg (=yes) Translate the sequences
Examples:
Translate DNA or RNA to amino acids in reading frame 1:
% alignment-translate < dna.fasta > aa.fasta
Give the reverse complement without translation:
% alignment-translate -rc --translate=no < dna.fasta > dna2.fasta
The following commands are identical:
% alignment-translate --frame=-2 < dna.fasta > aa2.fasta
% alignment-translate -rc --frame=2 < dna.fasta > aa2.fasta
-------
17/30 alignment-find --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-find --help
--- stdout ---
Find the last (or first) FASTA alignment in a file.
(Alignments are ended by blank lines.)
Usage: alignment-find [OPTIONS] < in-file
Allowed options:
-h [ --help ] produce help message
--alphabet arg Specify the alphabet: DNA, RNA, Amino-Acids,
Amino-Acids+stop, Triplets, Codons, or Codons+stop.
--first get the first alignment in the file
--last get the last alignment in the file (default)
-------
18/30 trees-consensus --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/trees-consensus --help
--- stdout ---
Find consensus trees and supported splits.
Usage: trees-consensus [OPTIONS] <sampled-trees> [<sampled-trees> ... <sampled-trees>]
Input options:
-h [ --help ] Produce help message.
-s [ --skip ] arg (=10%) Number of trees to skip.
-u [ --until ] arg Read until this number of trees.
-m [ --max ] arg Thin tree samples down to this number of trees.
-x [ --subsample ] arg (=1) Factor by which to subsample.
--ignore arg Comma-separated list of taxa to ignore.
Reporting options:
--map-trees arg (=1) Only report the top <arg> trees per file.
--map-tree arg Write out the map tree to file <arg>.
--min-support arg (=0.25) Minimum threshold PP for splits.
--report arg Write supported partitions to file <arg>.
--consensus-PP arg Write out consensus trees+PP.
--consensus arg Write out consensus trees.
--greedy-consensus arg Write out greedy consensus trees.
--extended-consensus-L arg Write out extended consensus trees + lengths.
--extended-consensus arg Write out extended consensus trees.
--support-levels arg Write #branches versus LOD to file <arg>.
--extended-support-levels arg Write #sub-branches versus LOD to file <arg>.
--odds-ratio arg (=1.5) Report partial-splits only if removing taxa
improves the odds by at least this ratio.
-v [ --verbose ] Output more log messages on stderr.
Search options:
--sub-partitions Search for partial splits.
--depth arg (=1) Depth at which to look for partial splits.
--rooting arg (=0.9) Threshold in search for partial splits.
Arguments for consensus trees are level1:filename1[,level2:filename2,...]
o each level is a minimum PP and should be in the range [0.5, 1.0].
o drop "filename" or specify ":-" to write to the terminal.
-------
19/30 tree-mean-lengths --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/tree-mean-lengths --help
--- stdout ---
Compute the mean lengths for branches in the given topology.
Usage: tree-mean-lengths <tree-file> < in-file
Allowed options:
-h [ --help ] produce help message
--tree arg tree to re-root
-s [ --skip ] arg (=0) number of tree samples to skip
-u [ --until ] arg Read until this number of trees.
--prune arg Comma-separated taxa to remove
--simple Ignore all branches not in the query tree
-x [ --subsample ] arg (=1) factor by which to sub-sample
--var report standard deviation of branch lengths
instead of mean
--no-node-lengths ignore branches not in the specified topology
--safe Don't die if no trees match the topology
--show-node-lengths Output special format
-v [ --verbose ] Output more log messages on stderr.
-------
20/30 mctree-mean-lengths --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/mctree-mean-lengths --help
--- stdout ---
Compute the mean lengths for branches in the given topology.
Usage: tree-mean-lengths <tree-file> < in-file
Allowed options:
-h [ --help ] produce help message
--tree arg tree to re-root
-s [ --skip ] arg (=0) number of tree samples to skip
-u [ --until ] arg Read until this number of trees.
--prune arg Comma-separated taxa to remove
-x [ --subsample ] arg (=1) factor by which to subsample
--var report standard deviation of branch lengths
instead of mean
--no-node-lengths ignore branches not in the specified topology
--safe Don't die if no trees match the topology
--drop-partial Remove partial branches
--seed arg random seed
-v [ --verbose ] Output more log messages on stderr.
-------
21/30 trees-to-SRQ --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/trees-to-SRQ --help
--- stdout ---
Generate Scaled Regeneration Quantile (SRQ) plot
Usage: tree-to-srq <predicates-file> < in-file
Allowed options:
-h [ --help ] produce help message
--predicates arg predicates to examine
-s [ --skip ] arg (=0) number of trees to skip
-x [ --subsample ] arg (=1) factor by which to sub-sample
-u [ --until ] arg Read until this number of trees.
--max-points arg maximum number of points to record
--mode arg (=SRQ) SRQ, sum, or values
--invert consider the inverse of each event instead
--no-scale-x don't scale X
--no-scale-y don't scale Y
-------
22/30 pickout --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/pickout --help
--- stdout ---
Generate table from key = value lines in file.
Usage: pickout [OPTIONS] <field1> [<field2> ... ] < <data-file>
All options:
-h [ --help ] Produce help message.
-n [ --no-header ] Suppress the line of field names.
--large The last value goes to the end of the line.
--multi-line The last continues until a blank line.
-------
23/30 cut-range --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/cut-range --help
--- stdout ---
Select lines between certain values of a key. (e.g. iterations)
Usage: cut-range [OPTIONS]
All options:
Invisible options:
--filenames arg Filenames to read
All options:
-h [ --help ] produce help message
--key arg (=iterations) cut based on values of <key>=value
--skip arg the number of samples to skip
--until arg last sample to use
--size arg maximum number of samples to use
--verbose Output more log messages on stderr.
-------
24/30 trees-distances --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/trees-distances --help
--- stdout ---
Compute autocorrelations or other functions of tree distances.
Usage: trees-distances <analysis> trees-file1 [trees-file2 ...]
All options:
Input options:
-h [ --help ] produce help message
-s [ --skip ] arg (=0) number of tree samples to skip
-u [ --until ] arg Read until this number of trees.
-m [ --max ] arg Thin tree samples down to this number of trees.
-x [ --subsample ] arg (=1) factor by which to subsample
-v [ --verbose ] Output more log messages on stderr.
Analysis options:
--analysis arg (=matrix) Analysis: matrix, autocorrelation, diameter,
compare, convergence, converged.
--metric arg (=topology) Tree distance: topology, branch,
internal-branch.
--remove-duplicates [matrix]: disallow zero distances between
points.
--max-lag arg [autocorrelation]: max lag to consider.
--CI arg (=0.95) Confidence interval size.
--converged arg (=0.05) Comma-separated quantiles of distance required
for converged? (smaller is more strict).
--mean Show mean and standard deviation
--median Show median and confidence interval
--minmax Show minimum and maximum distances
--leaves-only Show minimum and maximum distances
--topology-only Show minimum and maximum distances
--jitter arg Amount of noise to add to distances
-------
25/30 alignment-thin --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-thin --help
--- stdout ---
Remove sequences or columns from an alignment.
Usage: alignment-thin <alignment-file> [OPTIONS]
General options:
-h [ --help ] Print usage information.
-v [ --verbose ] Output more log messages on stderr.
Sequence filtering options:
--protect arg Sequences that cannot be removed (comma-separated).
--remove arg Remove sequences in comma-separated list <arg>.
--longer-than arg Remove sequences not longer than <arg>.
--shorter-than arg Remove sequences not shorter than <arg>.
--cutoff arg Remove similar sequences with #mismatches < cutoff.
--down-to arg Remove similar sequences down to <arg> sequences.
--remove-crazy arg Remove <arg> outlier sequences -- defined as
sequences that are missing too many conserved sites.
--conserved arg (=0.75) Fraction of sequences that must contain a letter for
it to be considered conserved.
Column filtering options:
--min-letters arg Remove columns with fewer than <arg> letters.
--remove-unique arg Remove insertions in a single sequence if longer than
<arg> letters
Output options:
--sort Sort partially ordered columns to group similar gaps.
--show-lengths Just print out sequence lengths.
--find-dups arg For each sequence, find the closest other sequence.
Examples:
Remove columns without a minimum number of letters:
% alignment-thin --min-letters=5 file.fasta > file-thinned.fasta
Remove sequences by name:
% alignment-thin --remove=seq1,seq2 file.fasta > file2.fasta
Remove short sequences:
% alignment-thin --longer-than=250 file.fasta > file-long.fasta
Remove sequences with <= 5 differences from the closest other sequence:
% alignment-thin --cutoff=5 file.fasta > more-than-5-differences.fasta
Like --cutoff, but stop when we have the right number of sequences:
% alignment-thin --down-to=30 file.fasta > file-30taxa.fasta
Remove dissimilar sequences that are missing conserved columns:
% alignment-thin --remove-crazy=10 file.fasta > file2.fasta
Protect some sequences from being removed:
% alignment-thin --down-to=30 file.fasta --protect=seq1,seq2 > file2.fasta
-------
26/30 alignments-diff --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignments-diff --help
--- stdout ---
Align two alignments for comparison.
Usage: alignments-diff alignment-file1 alignment-file2 [OPTIONS]
General options:
-h [ --help ] produce help message
Input options:
--alphabet arg set to 'Codons' to prefer codon alphabets
Output options:
--merge Stack the two alignments into one alignment
with duplicate names
--dual Write out the two aligned alignments separately
--fill arg (=gap) blank columns filled with: gap or unknown
-d [ --differences-file ] arg Filename to store differences in AU format
--blocksize arg (=20) Width of blocks of same color
--classes arg (=1) Number of groups for non-matching characters
-------
27/30 tree-tool --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/tree-tool --help
--- stdout ---
Perform various operations on Newick trees.
Usage: tree-tool <tree-file> [OPTIONS]
General options:
-h [ --help ] produce help message
-v [ --verbose ] Output more log messages on stderr.
Modification options:
--prune arg Comma-separated taxa to remove
--resolve Comma-separated taxa to remove
--remove-root-branch Remove single branch from root.
--remove-root-branches Ensure root is not a tip.
--remove-knuckles Remove degree-2 nodes.
Output options:
--scale arg Scale branch-lengths by factor
--length Report the total tree length
--diameter Report the total tree length
-------
28/30 alignment-distances --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/alignment-distances --help
--- stdout ---
Compute distances between alignments.
Usage: alignment-distances <analysis> alignments-file1 [alignments-file2 ...]
All options:
Input options:
-h [ --help ] Produce help message
-s [ --skip ] arg (=0) Number of alignment samples to skip.
-m [ --max ] arg (=1000) Maximum number of alignments to
analyze.
-v [ --verbose ] Output more log messages on stderr.
--alphabet arg Specify the alphabet: DNA, RNA,
Amino-Acids, Amino-Acids+stop,
Triplets, Codons, or Codons+stop.
Analysis options:
--distances arg (=splits:splits2:nonrecall:inaccuracy)
Colon-separated list of distances.
--analysis arg Analysis: score, AxA, NxN, compare,
median, distances
--CI arg (=0.94999999999999996) Confidence interval size.
--mean Show mean and standard deviation
--median Show median and confidence interval
--minmax Show minimum and maximum distances
Distances:
splits, splits2, pairwise, recall, accuracy, nonrecall, inaccuracy
Examples:
Compute distances from true.fasta to each in As.fasta:
% alignment-distances score true.fasta As.fasta
Compute distance matrix between all pairs of alignments in all files:
% alignment-distances AxA file1.fasta ... fileN.fasta
Compute all NxN pairwise alignment accuracies, averaged over As:
% alignment-distances NxN true.fasta As.fasta
Find alignment with smallest average distance to other alignments:
% alignment-distances median As.fasta A.fasta
Compare the distances with-in and between the two groups:
% alignment-distances compare A-dist1.fasta A-dist2.fasta
Report distribution of average distance to other alignments:
% alignment-distances distances As.fasta A.fasta
-------
29/30 subsample --help OK 0.01 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-subsample --help
--- stdout ---
Subsample lines in a file.
Usage: subsample [OPTIONS] < in-file
Allowed options:
-h [ --help ] produce help message
-x [ --factor ] arg (=1) Factor by which to subsample.
--skip arg (=0) Throw out some lines at the beginning.
--max arg Maximum number of samples to keep
--header This file has a header - don't throw it out.
-------
30/30 bali-phy testsuite OK 284.67 s
--- command ---
/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/tests/run-tests.py /<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/bali-phy --package-path=/<<BUILDDIR>>/bali-phy-3.4.1+dfsg/obj-arm-linux-gnueabihf/src/builtins:/<<BUILDDIR>>/bali-phy-3.4.1+dfsg
--- stdout ---
Running tests for 'bali-phy':
Running test: prob_prog/regression ... ok
Running test: prob_prog/order-two ... ok
Running test: prob_prog/lazy_sample ... ok
Running test: prob_prog/if-then-else/1 ... ok
Running test: prob_prog/functions/1 ... ok
Running test: print/2 ... ok
Running test: print/1 ... ok
Running test: parse/x3/5 ... ok
Running test: parse/x3/4 ... ok
Running test: parse/x3/3 ... ok
Running test: parse/x3/2 ... ok
Running test: parse/x3/1 ... ok
Running test: parse/partitions/link/9 ... ok
Running test: parse/partitions/link/8 ... ok
Running test: parse/partitions/link/7 ... ok
Running test: parse/partitions/link/6 ... ok
Running test: parse/partitions/link/5 ... ok
Running test: parse/partitions/link/4 ... ok
Running test: parse/partitions/link/3 ... ok
Running test: parse/partitions/link/2 ... ok
Running test: parse/partitions/link/1 ... ok
Running test: parse/partitions/4 ... ok
Running test: parse/partitions/3 ... ok
Running test: parse/partitions/2 ... ok
Running test: parse/partitions/1 ... ok
Running test: parse/let/1 ... ok
Running test: parse/int-to-double/3 ... ok
Running test: parse/int-to-double/2 ... ok
Running test: parse/int-to-double/1 ... ok
Running test: parse/guess-alphabet/rna ... ok
Running test: parse/guess-alphabet/dna ... ok
Running test: parse/guess-alphabet/aa ... ok
Running test: parse/guess-alphabet/Triplets/rna ... ok
Running test: parse/guess-alphabet/Triplets/dna ... ok
Running test: parse/guess-alphabet/Codons/rna ... ok
Running test: parse/guess-alphabet/Codons/dna ... ok
Running test: parse/error/4 ... ok
Running test: parse/error/3 ... ok
Running test: parse/error/2 ... ok
Running test: parse/error/1 ... ok
Running test: parse/constraints/1 ... FAIL! ['exit'] (expected)
evaluating reg # 8668 (unchangeable): Prelude:join <7580> <7571>
evaluating reg # 7572 (unchangeable): Prelude:add <7585> <8685>
Add: object 'SModel.MixtureModels %0' is not double, int, log_double, or char'
Running test: parse/M3/2 ... ok
Running test: parse/M3/1 ... ok
Running test: parse/9 ... ok
Running test: parse/8 ... ok
Running test: parse/7 ... ok
Running test: parse/6 ... ok
Running test: parse/5 ... ok
Running test: parse/4 ... ok
Running test: parse/3 ... ok
Running test: parse/26 ... ok
Running test: parse/25 ... ok
Running test: parse/24 ... ok
Running test: parse/23 ... ok
Running test: parse/22 ... ok
Running test: parse/21 ... ok
Running test: parse/19 ... ok
Running test: parse/18 ... ok
Running test: parse/17 ... ok
Running test: parse/16 ... ok
Running test: parse/14 ... ok
Running test: parse/13 ... ok
Running test: parse/12 ... ok
Running test: parse/11 ... ok
Running test: parse/10 ... ok
Running test: optimizer/pat-bind ... ok
Running test: optimizer/eta-reduction ... ok
Running test: optimizer/9 ... ok
Running test: optimizer/8 ... ok
Running test: optimizer/7 ... ok
Running test: optimizer/6 ... ok
Running test: optimizer/5 ... ok
Running test: optimizer/4 ... ok
Running test: optimizer/3 ... ok
Running test: optimizer/2 ... ok
Running test: optimizer/16 ... FAIL! ['error'] (expected)
Running test: optimizer/15 ... ok
Running test: optimizer/14 ... ok
Running test: optimizer/13 ... ok
Running test: optimizer/12 ... FAIL! ['error'] (expected)
Running test: optimizer/11 ... FAIL! ['error'] (expected)
Running test: optimizer/10 ... ok
Running test: optimizer/1 ... ok
Running test: mcmc/with-imodel ... ok
Running test: mcmc/two-sequences/1 ... ok
Running test: mcmc/one-sequence/1 ... ok
Running test: mcmc/no-imodel ... ok
Running test: mcmc/log-ancestral ... ok
Running test: mcmc/fixed-scale ... ok
Running test: IO/errors/Triplets/AUTGC ... ok
Running test: IO/errors/Triplets/2 ... ok
Running test: IO/errors/Triplets/1 ... ok
Running test: IO/errors/DNA-RNA/3 ... ok
Running test: IO/errors/DNA-RNA/2 ... ok
Running test: IO/errors/DNA-RNA/1 ... ok
Running test: IO/errors/Codons/stop/2 ... ok
Running test: IO/errors/Codons/stop/1 ... ok
Running test: IO/errors/Codons/AUTGC ... ok
Running test: IO/errors/Codons/3 ... ok
Running test: IO/errors/Codons/2 ... ok
Running test: IO/errors/Codons/1 ... ok
SUCCESS! (0 unexpected failures, 4 expected failures, 101 tests total)
-------
Ok: 29
Expected Fail: 0
Fail: 1
Unexpected Pass: 0
Skipped: 0
Timeout: 0
dh_auto_test: cd obj-arm-linux-gnueabihf && LC_ALL=C.UTF-8 MESON_TESTTHREADS=4 ninja test returned exit code 1
make: *** [debian/rules:20: build-arch] Error 255
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2
--------------------------------------------------------------------------------
Build finished at 2019-07-10T05:55:06Z
Finished
--------
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
E: Build failure (dpkg-buildpackage died)
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 108040
Build-Time: 784
Distribution: bullseye-staging
Fail-Stage: build
Host Architecture: armhf
Install-Time: 512
Job: bali-phy_3.4.1+dfsg-2
Machine Architecture: armhf
Package: bali-phy
Package-Time: 1318
Source-Version: 3.4.1+dfsg-2
Space: 108040
Status: attempted
Version: 3.4.1+dfsg-2
--------------------------------------------------------------------------------
Finished at 2019-07-10T05:55:06Z
Build needed 00:21:58, 108040k disk space