I: pbuilder: network access will be disabled during build I: Current time: Sun Jun 7 00:02:28 +14 2020 I: pbuilder-time-stamp: 1591437748 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [pdb2pqr_2.1.1+dfsg-5.dsc] I: copying [./pdb2pqr_2.1.1+dfsg.orig.tar.xz] I: copying [./pdb2pqr_2.1.1+dfsg-5.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Mon May 27 20:43:35 2019 +14 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./pdb2pqr_2.1.1+dfsg-5.dsc dpkg-source: info: extracting pdb2pqr in pdb2pqr-2.1.1+dfsg dpkg-source: info: unpacking pdb2pqr_2.1.1+dfsg.orig.tar.xz dpkg-source: info: unpacking pdb2pqr_2.1.1+dfsg-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying fix-hashbangs.patch dpkg-source: info: applying no_privacy_breach_logo.patch dpkg-source: info: applying do_not_try_to_build_removed_js_target.patch dpkg-source: info: applying fix_hardening_no_relro dpkg-source: info: applying fix_no_debug_symbols_warning dpkg-source: info: applying spelling.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/29518/tmp/hooks/D01_modify_environment starting debug: Running on cbxi4pro0. I: Changing host+domainname to test build reproducibility I: Adding a custom variable just for the fun of it... I: Changing /bin/sh to bash Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' I: Setting pbuilder2's login shell to /bin/bash I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other I: user script /srv/workspace/pbuilder/29518/tmp/hooks/D01_modify_environment finished I: user script /srv/workspace/pbuilder/29518/tmp/hooks/D02_print_environment starting I: set BASH=/bin/sh BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath BASH_ALIASES=() BASH_ARGC=() BASH_ARGV=() BASH_CMDS=() BASH_LINENO=([0]="12" [1]="0") BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") BASH_VERSION='5.0.3(1)-release' BUILDDIR=/build BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' BUILDUSERNAME=pbuilder2 BUILD_ARCH=armhf DEBIAN_FRONTEND=noninteractive DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4' DIRSTACK=() DISTRIBUTION= EUID=0 FUNCNAME=([0]="Echo" [1]="main") GROUPS=() HOME=/root HOSTNAME=i-capture-the-hostname HOSTTYPE=arm HOST_ARCH=armhf IFS=' ' INVOCATION_ID=21791f6d4fe34803acf2f3fe70979309 LANG=C LANGUAGE=it_CH:it LC_ALL=C MACHTYPE=arm-unknown-linux-gnueabihf MAIL=/var/mail/root OPTERR=1 OPTIND=1 OSTYPE=linux-gnueabihf PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path PBCURRENTCOMMANDLINEOPERATION=build PBUILDER_OPERATION=build PBUILDER_PKGDATADIR=/usr/share/pbuilder PBUILDER_PKGLIBDIR=/usr/lib/pbuilder PBUILDER_SYSCONFDIR=/etc PIPESTATUS=([0]="0") POSIXLY_CORRECT=y PPID=29518 PS4='+ ' PWD=/ SHELL=/bin/bash SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix SHLVL=3 SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.YzjtY1LDJF/pbuilderrc_nmvv --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.YzjtY1LDJF/b2 --logfile b2/build.log pdb2pqr_2.1.1+dfsg-5.dsc' SUDO_GID=115 SUDO_UID=111 SUDO_USER=jenkins TERM=unknown TZ=/usr/share/zoneinfo/Etc/GMT-14 UID=0 USER=root _='I: set' http_proxy=http://10.0.0.15:8000/ I: uname -a Linux i-capture-the-hostname 4.19.0-9-armmp #1 SMP Debian 4.19.118-2 (2020-04-29) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 18 2019 bash -rwxr-xr-x 3 root root 26052 Jul 11 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 11 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 11 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore -rwxr-xr-x 1 root root 22432 Mar 1 2019 cat -rwxr-xr-x 1 root root 38868 Mar 1 2019 chgrp -rwxr-xr-x 1 root root 38836 Mar 1 2019 chmod -rwxr-xr-x 1 root root 42972 Mar 1 2019 chown -rwxr-xr-x 1 root root 88376 Mar 1 2019 cp -rwxr-xr-x 1 root root 75516 Jan 18 2019 dash -rwxr-xr-x 1 root root 71648 Mar 1 2019 date -rwxr-xr-x 1 root root 51212 Mar 1 2019 dd -rwxr-xr-x 1 root root 55672 Mar 1 2019 df -rwxr-xr-x 1 root root 88444 Mar 1 2019 dir -rwxr-xr-x 1 root root 54872 Jan 10 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Mar 1 2019 echo -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep -rwxr-xr-x 1 root root 18260 Mar 1 2019 false -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 10 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 23 09:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 8 2019 grep -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 6 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 27 2018 hostname -rwxr-xr-x 1 root root 43044 Mar 1 2019 ln -rwxr-xr-x 1 root root 34932 Jul 27 2018 login -rwxr-xr-x 1 root root 88444 Mar 1 2019 ls -rwxr-xr-x 1 root root 67036 Jan 10 2019 lsblk -rwxr-xr-x 1 root root 47168 Mar 1 2019 mkdir -rwxr-xr-x 1 root root 43040 Mar 1 2019 mknod -rwxr-xr-x 1 root root 26552 Mar 1 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 10 2019 more -rwsr-xr-x 1 root root 34268 Jan 10 2019 mount -rwxr-xr-x 1 root root 9688 Jan 10 2019 mountpoint -rwxr-xr-x 1 root root 84284 Mar 1 2019 mv lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Mar 1 2019 pwd lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Mar 1 2019 readlink -rwxr-xr-x 1 root root 42968 Mar 1 2019 rm -rwxr-xr-x 1 root root 26496 Mar 1 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 22 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 23 2018 sed lrwxrwxrwx 1 root root 4 Jun 7 00:03 sh -> bash lrwxrwxrwx 1 root root 4 Jun 6 22:26 sh.distrib -> dash -rwxr-xr-x 1 root root 22384 Mar 1 2019 sleep -rwxr-xr-x 1 root root 51124 Mar 1 2019 stty -rwsr-xr-x 1 root root 42472 Jan 10 2019 su -rwxr-xr-x 1 root root 22392 Mar 1 2019 sync -rwxr-xr-x 1 root root 283324 Apr 24 2019 tar -rwxr-xr-x 1 root root 9808 Jan 22 2019 tempfile -rwxr-xr-x 1 root root 63464 Mar 1 2019 touch -rwxr-xr-x 1 root root 18260 Mar 1 2019 true -rwxr-xr-x 1 root root 9636 Apr 23 09:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 10 2019 umount -rwxr-xr-x 1 root root 22380 Mar 1 2019 uname -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress -rwxr-xr-x 1 root root 88444 Mar 1 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 10 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 22 2019 which lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew I: user script /srv/workspace/pbuilder/29518/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper (>= 11~), dh-python, gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper (>= 11~); however: Package debhelper is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on swig; however: Package swig is not installed. pbuilder-satisfydepends-dummy depends on xmlto; however: Package xmlto is not installed. pbuilder-satisfydepends-dummy depends on openbabel; however: Package openbabel is not installed. pbuilder-satisfydepends-dummy depends on python-dev; however: Package python-dev is not installed. pbuilder-satisfydepends-dummy depends on python-numpy; however: Package python-numpy is not installed. pbuilder-satisfydepends-dummy depends on scons; however: Package scons is not installed. pbuilder-satisfydepends-dummy depends on dos2unix; however: Package dos2unix is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} docbook-xml{a} docbook-xsl{a} dos2unix{a} dwz{a} file{a} fontconfig-config{a} fonts-dejavu-core{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcairo2{a} libcroco3{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libicu63{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libopenbabel5{a} libpipeline1{a} libpixman-1-0{a} libpng16-16{a} libpython-dev{a} libpython-stdlib{a} libpython2-dev{a} libpython2-stdlib{a} libpython2.7{a} libpython2.7-dev{a} libpython2.7-minimal{a} libpython2.7-stdlib{a} libpython3-stdlib{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} libsigsegv2{a} libssl1.1{a} libtool{a} libuchardet0{a} libx11-6{a} libx11-data{a} libxau6{a} libxcb-render0{a} libxcb-shm0{a} libxcb1{a} libxdmcp6{a} libxext6{a} libxml2{a} libxml2-utils{a} libxrender1{a} libxslt1.1{a} m4{a} man-db{a} mime-support{a} openbabel{a} po-debconf{a} python{a} python-dev{a} python-minimal{a} python-numpy{a} python-pkg-resources{a} python2{a} python2-dev{a} python2-minimal{a} python2.7{a} python2.7-dev{a} python2.7-minimal{a} python3{a} python3-distutils{a} python3-lib2to3{a} python3-minimal{a} python3.7{a} python3.7-minimal{a} readline-common{a} scons{a} sensible-utils{a} sgml-base{a} sgml-data{a} swig{a} swig3.0{a} ucf{a} xml-core{a} xmlto{a} xsltproc{a} The following packages are RECOMMENDED but will NOT be installed: curl dblatex fop libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libpaper-utils lynx shared-mime-info wget xdg-user-dirs zip 0 packages upgraded, 107 newly installed, 0 to remove and 0 not upgraded. Need to get 84.3 MB of archives. After unpacking 234 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libpython2.7-minimal armhf 2.7.16-2+deb10u1 [395 kB] Get: 8 http://deb.debian.org/debian buster/main armhf python2.7-minimal armhf 2.7.16-2+deb10u1 [1171 kB] Get: 9 http://deb.debian.org/debian buster/main armhf python2-minimal armhf 2.7.16-1 [41.4 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python-minimal armhf 2.7.16-1 [21.0 kB] Get: 11 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython2.7-stdlib armhf 2.7.16-2+deb10u1 [1837 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python2.7 armhf 2.7.16-2+deb10u1 [305 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython2-stdlib armhf 2.7.16-1 [20.8 kB] Get: 19 http://deb.debian.org/debian buster/main armhf libpython-stdlib armhf 2.7.16-1 [20.8 kB] Get: 20 http://deb.debian.org/debian buster/main armhf python2 armhf 2.7.16-1 [41.6 kB] Get: 21 http://deb.debian.org/debian buster/main armhf python armhf 2.7.16-1 [22.8 kB] Get: 22 http://deb.debian.org/debian buster/main armhf libpython3.7-minimal armhf 3.7.3-2+deb10u1 [582 kB] Get: 23 http://deb.debian.org/debian buster/main armhf python3.7-minimal armhf 3.7.3-2+deb10u1 [1465 kB] Get: 24 http://deb.debian.org/debian buster/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libmpdec2 armhf 2.4.2-2 [69.3 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libpython3.7-stdlib armhf 3.7.3-2+deb10u1 [1660 kB] Get: 27 http://deb.debian.org/debian buster/main armhf python3.7 armhf 3.7.3-2+deb10u1 [330 kB] Get: 28 http://deb.debian.org/debian buster/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB] Get: 29 http://deb.debian.org/debian buster/main armhf python3 armhf 3.7.3-1 [61.5 kB] Get: 30 http://deb.debian.org/debian buster/main armhf sgml-base all 1.29 [14.8 kB] Get: 31 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 34 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 35 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 36 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 38 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 39 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 40 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 41 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 42 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 44 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 47 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 49 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 54 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 55 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 56 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 57 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 58 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 59 http://deb.debian.org/debian buster/main armhf python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 60 http://deb.debian.org/debian buster/main armhf python3-distutils all 3.7.3-1 [142 kB] Get: 61 http://deb.debian.org/debian buster/main armhf dh-python all 3.20190308 [99.3 kB] Get: 62 http://deb.debian.org/debian buster/main armhf xml-core all 0.18+nmu1 [23.8 kB] Get: 63 http://deb.debian.org/debian buster/main armhf sgml-data all 2.0.11 [179 kB] Get: 64 http://deb.debian.org/debian buster/main armhf docbook-xml all 4.5-8 [84.7 kB] Get: 65 http://deb.debian.org/debian buster/main armhf docbook-xsl all 1.79.1+dfsg-2 [1249 kB] Get: 66 http://deb.debian.org/debian buster/main armhf dos2unix armhf 7.4.0-1 [387 kB] Get: 67 http://deb.debian.org/debian buster/main armhf fonts-dejavu-core all 2.37-1 [1068 kB] Get: 68 http://deb.debian.org/debian buster/main armhf fontconfig-config all 2.13.1-2 [280 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libgfortran-8-dev armhf 8.3.0-6 [260 kB] Get: 71 http://deb.debian.org/debian buster/main armhf gfortran-8 armhf 8.3.0-6 [7219 kB] Get: 72 http://deb.debian.org/debian buster/main armhf gfortran armhf 4:8.3.0-1 [1424 B] Get: 73 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 75 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libfontconfig1 armhf 2.13.1-2 [328 kB] Get: 77 http://deb.debian.org/debian buster/main armhf libpixman-1-0 armhf 0.36.0-1 [465 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB] Get: 79 http://deb.debian.org/debian buster/main armhf libxdmcp6 armhf 1:1.1.2-3 [24.9 kB] Get: 80 http://deb.debian.org/debian buster/main armhf libxcb1 armhf 1.13.1-2 [132 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libx11-data all 2:1.6.7-1 [298 kB] Get: 82 http://deb.debian.org/debian buster/main armhf libx11-6 armhf 2:1.6.7-1 [698 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB] Get: 84 http://deb.debian.org/debian buster/main armhf libxcb-shm0 armhf 1.13.1-2 [99.0 kB] Get: 85 http://deb.debian.org/debian buster/main armhf libxext6 armhf 2:1.3.3-1+b2 [48.1 kB] Get: 86 http://deb.debian.org/debian buster/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB] Get: 87 http://deb.debian.org/debian buster/main armhf libcairo2 armhf 1.16.0-4 [616 kB] Get: 88 http://deb.debian.org/debian buster/main armhf libexpat1-dev armhf 2.2.6-2+deb10u1 [126 kB] Get: 89 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 90 http://deb.debian.org/debian buster/main armhf libopenbabel5 armhf 2.4.1+dfsg-3 [2634 kB] Get: 91 http://deb.debian.org/debian buster/main armhf libpython2.7 armhf 2.7.16-2+deb10u1 [892 kB] Get: 92 http://deb.debian.org/debian buster/main armhf libpython2.7-dev armhf 2.7.16-2+deb10u1 [31.0 MB] Get: 93 http://deb.debian.org/debian buster/main armhf libpython2-dev armhf 2.7.16-1 [20.9 kB] Get: 94 http://deb.debian.org/debian buster/main armhf libpython-dev armhf 2.7.16-1 [20.9 kB] Get: 95 http://deb.debian.org/debian buster/main armhf libxml2-utils armhf 2.9.4+dfsg1-7+b3 [98.1 kB] Get: 96 http://deb.debian.org/debian buster/main armhf libxslt1.1 armhf 1.1.32-2.2~deb10u1 [217 kB] Get: 97 http://deb.debian.org/debian buster/main armhf openbabel armhf 2.4.1+dfsg-3 [117 kB] Get: 98 http://deb.debian.org/debian buster/main armhf python2.7-dev armhf 2.7.16-2+deb10u1 [291 kB] Get: 99 http://deb.debian.org/debian buster/main armhf python2-dev armhf 2.7.16-1 [1216 B] Get: 100 http://deb.debian.org/debian buster/main armhf python-dev armhf 2.7.16-1 [1192 B] Get: 101 http://deb.debian.org/debian buster/main armhf python-pkg-resources all 40.8.0-1 [182 kB] Get: 102 http://deb.debian.org/debian buster/main armhf python-numpy armhf 1:1.16.2-1 [1885 kB] Get: 103 http://deb.debian.org/debian buster/main armhf scons all 3.0.1-2 [538 kB] Get: 104 http://deb.debian.org/debian buster/main armhf swig3.0 armhf 3.0.12-2 [1342 kB] Get: 105 http://deb.debian.org/debian buster/main armhf swig armhf 3.0.12-2 [310 kB] Get: 106 http://deb.debian.org/debian buster/main armhf xsltproc armhf 1.1.32-2.2~deb10u1 [121 kB] Get: 107 http://deb.debian.org/debian buster/main armhf xmlto armhf 0.0.28-2.1 [32.5 kB] Fetched 84.3 MB in 8s (10.2 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../02-libuchardet0_0.0.6-3_armhf.deb ... 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Selecting previously unselected package python2. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20397 files and directories currently installed.) Preparing to unpack .../python2_2.7.16-1_armhf.deb ... Unpacking python2 (2.7.16-1) ... Setting up python-minimal (2.7.16-1) ... Selecting previously unselected package python. (Reading database ... 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Preparing to unpack .../python3.7-minimal_3.7.3-2+deb10u1_armhf.deb ... Unpacking python3.7-minimal (3.7.3-2+deb10u1) ... Setting up libssl1.1:armhf (1.1.1d-0+deb10u3) ... Setting up libpython3.7-minimal:armhf (3.7.3-2+deb10u1) ... Setting up libexpat1:armhf (2.2.6-2+deb10u1) ... Setting up python3.7-minimal (3.7.3-2+deb10u1) ... Selecting previously unselected package python3-minimal. (Reading database ... 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Unpacking libpython3.7-stdlib:armhf (3.7.3-2+deb10u1) ... Selecting previously unselected package python3.7. Preparing to unpack .../python3.7_3.7.3-2+deb10u1_armhf.deb ... Unpacking python3.7 (3.7.3-2+deb10u1) ... Selecting previously unselected package libpython3-stdlib:armhf. Preparing to unpack .../libpython3-stdlib_3.7.3-1_armhf.deb ... Unpacking libpython3-stdlib:armhf (3.7.3-1) ... Setting up python3-minimal (3.7.3-1) ... Selecting previously unselected package python3. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 21096 files and directories currently installed.) Preparing to unpack .../00-python3_3.7.3-1_armhf.deb ... Unpacking python3 (3.7.3-1) ... Selecting previously unselected package sgml-base. Preparing to unpack .../01-sgml-base_1.29_all.deb ... Unpacking sgml-base (1.29) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.12_all.deb ... Unpacking sensible-utils (0.0.12) ... 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Unpacking libglib2.0-0:armhf (2.58.3-2+deb10u2) ... Selecting previously unselected package libicu63:armhf. Preparing to unpack .../22-libicu63_63.1-6+deb10u1_armhf.deb ... Unpacking libicu63:armhf (63.1-6+deb10u1) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../23-libxml2_2.9.4+dfsg1-7+b3_armhf.deb ... Unpacking libxml2:armhf (2.9.4+dfsg1-7+b3) ... Selecting previously unselected package libcroco3:armhf. Preparing to unpack .../24-libcroco3_0.6.12-3_armhf.deb ... Unpacking libcroco3:armhf (0.6.12-3) ... Selecting previously unselected package libncurses6:armhf. Preparing to unpack .../25-libncurses6_6.1+20181013-2+deb10u2_armhf.deb ... Unpacking libncurses6:armhf (6.1+20181013-2+deb10u2) ... Selecting previously unselected package gettext. Preparing to unpack .../26-gettext_0.19.8.1-9_armhf.deb ... Unpacking gettext (0.19.8.1-9) ... Selecting previously unselected package intltool-debian. 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Selecting previously unselected package libgfortran5:armhf. Preparing to unpack .../40-libgfortran5_8.3.0-6_armhf.deb ... Unpacking libgfortran5:armhf (8.3.0-6) ... Selecting previously unselected package libgfortran-8-dev:armhf. Preparing to unpack .../41-libgfortran-8-dev_8.3.0-6_armhf.deb ... Unpacking libgfortran-8-dev:armhf (8.3.0-6) ... Selecting previously unselected package gfortran-8. Preparing to unpack .../42-gfortran-8_8.3.0-6_armhf.deb ... Unpacking gfortran-8 (8.3.0-6) ... Selecting previously unselected package gfortran. Preparing to unpack .../43-gfortran_4%3a8.3.0-1_armhf.deb ... Unpacking gfortran (4:8.3.0-1) ... Selecting previously unselected package libblas3:armhf. Preparing to unpack .../44-libblas3_3.8.0-2_armhf.deb ... Unpacking libblas3:armhf (3.8.0-2) ... Selecting previously unselected package libpng16-16:armhf. Preparing to unpack .../45-libpng16-16_1.6.36-6_armhf.deb ... Unpacking libpng16-16:armhf (1.6.36-6) ... 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Setting up xmlto (0.0.28-2.1) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/pdb2pqr-2.1.1+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package pdb2pqr dpkg-buildpackage: info: source version 2.1.1+dfsg-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with python2 debian/rules override_dh_auto_clean make[1]: Entering directory '/build/pdb2pqr-2.1.1+dfsg' ( cd pdb2pka && \ if [ -e pMC_mult_wrap.cpp.saved ]; then mv pMC_mult_wrap.cpp.saved pMC_mult_wrap.cpp; fi && \ if [ -e pMC_mult.py.saved ]; then mv pMC_mult.py.saved pMC_mult.py; fi ) find . -name *.pyc -delete find . -name *.so -delete find . -name *.os -delete rm -f *.cgi .sconsign.dblite .variables.cache pdb2pqr.py html/server.html src/aconf.py dh_auto_clean make[1]: Leaving directory '/build/pdb2pqr-2.1.1+dfsg' dh_clean debian/rules build dh build --with python2 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/pdb2pqr-2.1.1+dfsg' dh_auto_configure ( cd pdb2pka && \ cp -a pMC_mult_wrap.cpp pMC_mult_wrap.cpp.saved && \ cp -a pMC_mult.py pMC_mult.py.saved && \ swig -c++ -python -o pMC_mult_wrap.cpp pMC_mult.i ) python scons/scons.py \ URL="http://localhost/pdb2pqr/" \ PREFIX="/usr/share/pdb2pqr" scons: Reading SConscript files ... not using opal scons: done reading SConscript files. scons: Building targets ... CopySubAction("pdb2pqr.py", "pdb2pqr.py.in") Chmod("pdb2pqr.py", 0755) CopySubAction("apbs_cgi.cgi", "apbs_cgi.py") Chmod("apbs_cgi.cgi", 0755) CopySubAction("visualize.cgi", "visualize.py") Chmod("visualize.cgi", 0755) CopySubAction("querystatus.cgi", "querystatus.py") Chmod("querystatus.cgi", 0755) CopySubAction("src/aconf.py", "src/aconf.py.in") CopySubAction("html/server.html", "html/server.html.in") Copy("pdb2pqr.cgi", "pdb2pqr.py") g++ -o pdb2pka/substruct/Algorithms.os -c -g -fPIC -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/substruct/Algorithms.cpp In file included from /usr/include/python2.7/numpy/ndarraytypes.h:1822, from /usr/include/python2.7/numpy/ndarrayobject.h:12, from /usr/include/python2.7/numpy/arrayobject.h:4, from pdb2pka/substruct/Algorithms.cpp:43: /usr/include/python2.7/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ g++ -o pdb2pka/substruct/Algorithms.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib -lpython2.7 g++ -o pdb2pka/pMC_mult.os -c -g -fPIC -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/pMC_mult.cpp In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult.cpp:6: /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]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} 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 = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult.cpp:6: /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]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from pdb2pka/pMC_mult.h:9, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:61, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from pdb2pka/pMC_mult.h:9, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from pdb2pka/pMC_mult.h:9, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from pdb2pka/pMC_mult.h:9, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from pdb2pka/pMC_mult.h:9, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from pdb2pka/pMC_mult.h:9, from pdb2pka/pMC_mult.cpp:6: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ g++ -o pdb2pka/pMC_mult_wrap.os -c -g -fPIC -I/usr/include/python2.7 -I/usr/lib/python2.7/dist-packages/numpy/core/include pdb2pka/pMC_mult_wrap.cpp pdb2pka/pMC_mult_wrap.cpp: In function 'std::vector::iterator std_vector_Sl_double_Sg__erase__SWIG_0(std::vector*, std::vector::iterator)': pdb2pka/pMC_mult_wrap.cpp:5089:44: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__erase__SWIG_0(std::vector< double > *self,std::vector< double >::iterator pos){ return self->erase(pos); } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp:5089:171: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__erase__SWIG_0(std::vector< double > *self,std::vector< double >::iterator pos){ return self->erase(pos); } ^ pdb2pka/pMC_mult_wrap.cpp: In function 'std::vector::iterator std_vector_Sl_double_Sg__erase__SWIG_1(std::vector*, std::vector::iterator, std::vector::iterator)': pdb2pka/pMC_mult_wrap.cpp:5090:44: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__erase__SWIG_1(std::vector< double > *self,std::vector< double >::iterator first,std::vector< double >::iterator last){ return self->erase(first, last); } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp:5090:44: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 pdb2pka/pMC_mult_wrap.cpp:5090:218: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__erase__SWIG_1(std::vector< double > *self,std::vector< double >::iterator first,std::vector< double >::iterator last){ return self->erase(first, last); } ^ pdb2pka/pMC_mult_wrap.cpp: In function 'std::vector::iterator std_vector_Sl_double_Sg__insert__SWIG_0(std::vector*, std::vector::iterator, const value_type&)': pdb2pka/pMC_mult_wrap.cpp:5091:44: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__insert__SWIG_0(std::vector< double > *self,std::vector< double >::iterator pos,std::vector< double >::value_type const &x){ return self->insert(pos, x); } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp:5091:219: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SWIGINTERN std::vector< double >::iterator std_vector_Sl_double_Sg__insert__SWIG_0(std::vector< double > *self,std::vector< double >::iterator pos,std::vector< double >::value_type const &x){ return self->insert(pos, x); } ^ pdb2pka/pMC_mult_wrap.cpp: In function 'void std_vector_Sl_double_Sg__insert__SWIG_1(std::vector*, std::vector::iterator, std::vector::size_type, const value_type&)': pdb2pka/pMC_mult_wrap.cpp:5092:17: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SWIGINTERN void std_vector_Sl_double_Sg__insert__SWIG_1(std::vector< double > *self,std::vector< double >::iterator pos,std::vector< double >::size_type n,std::vector< double >::value_type const &x){ self->insert(pos, n, x); } ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp:5092:223: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SWIGINTERN void std_vector_Sl_double_Sg__insert__SWIG_1(std::vector< double > *self,std::vector< double >::iterator pos,std::vector< double >::size_type n,std::vector< double >::value_type const &x){ self->insert(pos, n, x); } ^ pdb2pka/pMC_mult_wrap.cpp: In function 'PyObject* _wrap_DoubleVector_erase__SWIG_0(PyObject*, PyObject*)': pdb2pka/pMC_mult_wrap.cpp:9290:60: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 result = std_vector_Sl_double_Sg__erase__SWIG_0(arg1,arg2); ^ pdb2pka/pMC_mult_wrap.cpp: In function 'PyObject* _wrap_DoubleVector_erase__SWIG_1(PyObject*, PyObject*)': pdb2pka/pMC_mult_wrap.cpp:9343:65: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 result = std_vector_Sl_double_Sg__erase__SWIG_1(arg1,arg2,arg3); ^ pdb2pka/pMC_mult_wrap.cpp: In function 'PyObject* _wrap_DoubleVector_insert__SWIG_0(PyObject*, PyObject*)': pdb2pka/pMC_mult_wrap.cpp:9753:83: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 result = std_vector_Sl_double_Sg__insert__SWIG_0(arg1,arg2,(double const &)*arg3); ^ pdb2pka/pMC_mult_wrap.cpp: In function 'PyObject* _wrap_DoubleVector_insert__SWIG_1(PyObject*, PyObject*)': pdb2pka/pMC_mult_wrap.cpp:9810:42: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 std_vector_Sl_double_Sg__insert__SWIG_1(arg1,arg2,arg3,(double const &)*arg4); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:463:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__x.begin(), __x.end(), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp: In function 'swig::SwigPyIterator* swig::make_output_iterator(const OutIter&, const OutIter&, const OutIter&, PyObject*) [with OutIter = __gnu_cxx::__normal_iterator >]': pdb2pka/pMC_mult_wrap.cpp:4441:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return new SwigPyIteratorClosed_T(current, begin, end, seq); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp:4441:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pdb2pka/pMC_mult_wrap.cpp: In function 'Sequence* swig::getslice(const Sequence*, Difference, Difference, Py_ssize_t) [with Sequence = std::vector; Difference = int]': pdb2pka/pMC_mult_wrap.cpp:4106:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return new Sequence(sb, se); ^~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::setslice(Sequence*, Difference, Difference, Py_ssize_t, const InputSeq&) [with Sequence = std::vector; Difference = int; InputSeq = std::vector]': pdb2pka/pMC_mult_wrap.cpp:4152:33: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 self->insert(std::copy(is.begin(), isit, sb), isit, is.end()); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp:4152:11: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 self->insert(std::copy(is.begin(), isit, sb), isit, is.end()); ^~~~ pdb2pka/pMC_mult_wrap.cpp:4152:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pdb2pka/pMC_mult_wrap.cpp:4159:11: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 self->erase(sb,se); ^~~~ pdb2pka/pMC_mult_wrap.cpp:4162:11: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 self->insert(sb, is.begin(), is.end()); ^~~~ pdb2pka/pMC_mult_wrap.cpp:4162:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::delslice(Sequence*, Difference, Difference, Py_ssize_t) [with Sequence = std::vector; Difference = int]': pdb2pka/pMC_mult_wrap.cpp:4211:9: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 self->erase(sb,se); ^~~~ pdb2pka/pMC_mult_wrap.cpp:4216:14: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 it = self->erase(it); pdb2pka/pMC_mult_wrap.cpp:4228:9: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 it = typename Sequence::reverse_iterator(self->erase((++it).base())); ^~ pdb2pka/pMC_mult_wrap.cpp:4228:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::erase(Sequence*, const typename Sequence::iterator&) [with Sequence = std::vector]': pdb2pka/pMC_mult_wrap.cpp:4082:5: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 seq->erase(position); ^~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1085:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(end(), __x); ^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(std::vector<_Tp, _Alloc>::const_iterator) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1317:7: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 erase(const_iterator __position) ^~~~~ /usr/include/c++/8/bits/stl_vector.h:1318:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return _M_erase(begin() + (__position - cbegin())); } ^ /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::const_iterator) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1344:7: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 erase(const_iterator __first, const_iterator __last) ^~~~~ /usr/include/c++/8/bits/stl_vector.h:1344:7: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1348:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); ^ In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:118:5: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:142:6: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_insert_aux(__pos, std::move(__x_copy._M_val())); ^~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:149:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(begin() + (__position - cbegin()), __x); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1222:7: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 insert(const_iterator __position, size_type __n, const value_type& __x) ^~~~~~ /usr/include/c++/8/bits/stl_vector.h:1225:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(begin() + __offset, __n, __x); ^~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp: In function 'swig::SwigPyIterator* swig::make_output_iterator(const OutIter&, PyObject*) [with OutIter = __gnu_cxx::__normal_iterator >]': pdb2pka/pMC_mult_wrap.cpp:4448:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return new SwigPyIteratorOpen_T(current, seq); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::reverse_iterator std::vector<_Tp, _Alloc>::rbegin() [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:735:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return reverse_iterator(end()); } ^ /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::reverse_iterator std::vector<_Tp, _Alloc>::rend() [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:753:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return reverse_iterator(begin()); } ^ /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::resize(std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:847:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_fill_insert(end(), __new_size - size(), __x); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::reserve(std::vector<_Tp, _Alloc>::size_type) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:74:12: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__n, ^~~~~ /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:214:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(), ^~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy(std::copy(__x.begin(), __x.end(), begin()), ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ end(), _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:226:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIteratorClosed_T::SwigPyIteratorClosed_T(swig::SwigPyIteratorClosed_T::out_iterator, swig::SwigPyIteratorClosed_T::out_iterator, swig::SwigPyIteratorClosed_T::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator >; ValueType = double; FromOper = swig::from_oper]': pdb2pka/pMC_mult_wrap.cpp:4390:5: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator >, double, swig::from_oper >::out_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SwigPyIteratorClosed_T(out_iterator curr, out_iterator first, out_iterator last, PyObject *seq) ^~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp:4390:5: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator >, double, swig::from_oper >::out_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 pdb2pka/pMC_mult_wrap.cpp:4390:5: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator >, double, swig::from_oper >::out_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 pdb2pka/pMC_mult_wrap.cpp:4391:73: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator >, double, swig::from_oper >::out_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 : SwigPyIterator_T(curr, seq), begin(first), end(last) ^ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 vector(_InputIterator __first, _InputIterator __last, ^~~~~~ /usr/include/c++/8/bits/stl_vector.h:543:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:546:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { _M_initialize_dispatch(__first, __last, __false_type()); } ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::const_reverse_iterator std::vector<_Tp, _Alloc>::rbegin() const [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:744:44: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return const_reverse_iterator(end()); } ^ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1266:2: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 insert(const_iterator __position, _InputIterator __first, ^~~~~~ /usr/include/c++/8/bits/stl_vector.h:1266:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1266:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1270:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_insert_dispatch(begin() + __offset, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1270:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_iterator.h: In constructor 'std::reverse_iterator<_Iterator>::reverse_iterator(std::reverse_iterator<_Iterator>::iterator_type) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_iterator.h:133:7: note: parameter passing for argument of type 'std::reverse_iterator<__gnu_cxx::__normal_iterator > >::iterator_type' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 reverse_iterator(iterator_type __x) : current(__x) { } ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /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]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /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 = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:159:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/vector.tcc:163:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _GLIBCXX_MOVE3(__position + 1, end(), __position); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /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, std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:172:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/vector.tcc:178:6: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _GLIBCXX_MOVE3(__last, end(), __first); ^~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_aux(std::vector<_Tp, _Alloc>::iterator, _Arg&&) [with _Arg = double; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:382:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} 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 = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:478:5: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIteratorOpen_T::SwigPyIteratorOpen_T(swig::SwigPyIteratorOpen_T::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator >; ValueType = double; FromOper = swig::from_oper]': pdb2pka/pMC_mult_wrap.cpp:4347:5: note: parameter passing for argument of type 'swig::SwigPyIteratorOpen_T<__gnu_cxx::__normal_iterator >, double, swig::from_oper >::out_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SwigPyIteratorOpen_T(out_iterator curr, PyObject *seq) ^~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp:4348:48: note: parameter passing for argument of type 'swig::SwigPyIteratorOpen_T<__gnu_cxx::__normal_iterator >, double, swig::from_oper >::out_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 : SwigPyIterator_T(curr, seq) ^ In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_assign(std::size_t, const value_type&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:255:13: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::fill(begin(), end(), __val); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = std::move_iterator; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_allocate_and_copy(size_type __n, ^~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1395:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1401:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, __result, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:62, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double]': /usr/include/c++/8/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Destroy(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~ /usr/include/c++/8/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_construct.h:206:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Destroy(__first, __last); ~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIterator_T::SwigPyIterator_T(swig::SwigPyIterator_T::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator >]': pdb2pka/pMC_mult_wrap.cpp:4289:5: note: parameter passing for argument of type 'swig::SwigPyIterator_T<__gnu_cxx::__normal_iterator > >::out_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 SwigPyIterator_T(out_iterator curr, PyObject *seq) ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::_M_initialize_dispatch(_InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1432:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_initialize_dispatch(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1432:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1437:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_range_initialize(__first, __last, _IterCategory()); ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_iterator.h: In constructor 'std::reverse_iterator<_Iterator>::reverse_iterator(std::reverse_iterator<_Iterator>::iterator_type) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_iterator.h:133:7: note: parameter passing for argument of type 'std::reverse_iterator<__gnu_cxx::__normal_iterator > >::iterator_type' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 reverse_iterator(iterator_type __x) : current(__x) { } ^~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/cmath:42, from /usr/include/c++/8/math.h:36, from /usr/include/python2.7/pyport.h:325, from /usr/include/python2.7/Python.h:61, from pdb2pka/pMC_mult_wrap.cpp:173: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(std::vector<_Tp, _Alloc>::iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1546:2: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 _M_insert_dispatch(iterator __pos, _InputIterator __first, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1546:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1546:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1549:4: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} 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 >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_if_noexcept_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:311:2: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a ~~~~~~~~~~~~~~~~~~~~~~~~~~~ (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::move(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:479:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 move(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:479:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:479:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:487:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__copy_move_a2(std::__miter_base(__first), ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ std::__miter_base(__last), __result); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator]': /usr/include/c++/8/bits/stl_uninitialized.h:297:41: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy_a(_GLIBCXX_MAKE_MOVE_ITERATOR(__first), ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ _GLIBCXX_MAKE_MOVE_ITERATOR(__last), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result, __alloc); ~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_algobase.h: In function 'void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double]': /usr/include/c++/8/bits/stl_algobase.h:724:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 fill(_ForwardIterator __first, _ForwardIterator __last, const _Tp& __value) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:724:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator; _ForwardIterator = double*; _Tp = double]': /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninitialized_copy_a(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:287:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:289:37: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::uninitialized_copy(__first, __last, __result); } ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:62, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_construct.h:127:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _Destroy(_ForwardIterator __first, _ForwardIterator __last) ^~~~~~~~ /usr/include/c++/8/bits/stl_construct.h:127:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_construct.h:137:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::_Destroy_aux<__has_trivial_destructor(_Value_type)>:: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __destroy(__first, __last); ~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1462:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_range_initialize(_ForwardIterator __first, _ForwardIterator __last, ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1462:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_vector.h:1465:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 const size_type __n = std::distance(__first, __last); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_vector.h:1469:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__first, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ this->_M_impl._M_start, ~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it) ^~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector]': /usr/include/c++/8/bits/stl_iterator.h:987:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/vector.tcc: In member 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 >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:672:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} 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 >' 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 >' changed in GCC 7.1 /usr/include/c++/8/bits/vector.tcc:678:41: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 const size_type __n = std::distance(__first, __last); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:695:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::copy(__first, __last, __position); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:702:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::__uninitialized_copy_a(__mid, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ this->_M_impl._M_finish, ~~~~~~~~~~~~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:713:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 std::copy(__first, __mid, __position); ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:729:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 = std::__uninitialized_copy_a(__first, __last, ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ __new_finish, ~~~~~~~~~~~~~ _M_get_Tp_allocator()); ~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/cmath:42, from /usr/include/c++/8/math.h:36, from /usr/include/python2.7/pyport.h:325, from /usr/include/python2.7/Python.h:61, from pdb2pka/pMC_mult_wrap.cpp:173: /usr/include/c++/8/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/cpp_type_traits.h:419:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __miter_base(_Iterator __it) ^~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = true; _II = __gnu_cxx::__normal_iterator >; _OI = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::assign(const SwigPySeq&, Seq*) [with SwigPySeq = swig::SwigPySequence_Cont; Seq = std::vector]': pdb2pka/pMC_mult_wrap.cpp:4739:7: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 seq->insert(seq->end(),(value_type)(*it)); ^~~ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 uninitialized_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:134:15: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 return std::__uninitialized_copy<__is_trivial(_ValueType1) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __is_trivial(_ValueType2) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ && __assignable>:: ~~~~~~~~~~~~~~~~~~ __uninit_copy(__first, __last, __result); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:62, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_construct.h: In static member function 'static void std::_Destroy_aux::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_construct.h:117:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __destroy(_ForwardIterator, _ForwardIterator) { } ^~~~~~~~~ /usr/include/c++/8/bits/stl_construct.h:117:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_algobase.h:455:8: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return (std::__copy_move_a2<__is_move_iterator<_II>::__value> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (std::__miter_base(__first), std::__miter_base(__last), ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __result)); ~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:66, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_iterator_base_funcs.h: In function 'typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 distance(_InputIterator __first, _InputIterator __last) ^~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_iterator_base_funcs.h:141:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__distance(__first, __last, ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/vector:64, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/stl_vector.h:1180:7: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 insert(const_iterator __position, value_type&& __x) ^~~~~~ /usr/include/c++/8/bits/stl_vector.h:1181:57: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 { return _M_insert_rval(__position, std::move(__x)); } ^ In file included from /usr/include/c++/8/vector:63, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator; _ForwardIterator = double*]': /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __uninit_copy(_InputIterator __first, _InputIterator __last, ^~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 /usr/include/c++/8/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 { return std::copy(__first, __last, __result); } ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator >; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __copy_move_a2(_II __first, _II __last, _OI __result) ^~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_algobase.h:420:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/bits/stl_algobase.h:66, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_iterator_base_funcs.h: In function 'constexpr typename std::iterator_traits<_Iterator>::difference_type std::__distance(_RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __distance(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /usr/include/c++/8/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_insert_rval(std::vector<_Tp, _Alloc>::const_iterator, std::vector<_Tp, _Alloc>::value_type&&) [with _Tp = double; _Alloc = std::allocator]': /usr/include/c++/8/bits/vector.tcc:327:5: note: parameter passing for argument of type 'std::vector::const_iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:341:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_insert_aux(begin() + __n, std::move(__v)); ^~~~~~~~~~~~~ /usr/include/c++/8/bits/vector.tcc:343:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 _M_realloc_insert(begin() + __n, std::move(__v)); ^~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator; _OI = double*]': /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 copy(_II __first, _II __last, _OI __result) ^~~~ /usr/include/c++/8/bits/stl_algobase.h:446:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 In file included from /usr/include/c++/8/vector:69, from pdb2pka/pMC_mult.h:10, from pdb2pka/pMC_mult_wrap.cpp:3148: /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]': /usr/include/c++/8/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector::iterator' {aka '__gnu_cxx::__normal_iterator >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:67, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_iterator.h: In function 'decltype (std::__miter_base(__it.base())) std::__miter_base(std::move_iterator<_IteratorL>) [with _Iterator = double*]': /usr/include/c++/8/bits/stl_iterator.h:1238:5: note: parameter passing for argument of type 'std::move_iterator' changed in GCC 7.1 __miter_base(move_iterator<_Iterator> __it) ^~~~~~~~~~~~ pdb2pka/pMC_mult_wrap.cpp: In member function 'ptrdiff_t swig::SwigPyIterator_T::distance(const swig::SwigPyIterator&) const [with OutIterator = __gnu_cxx::__normal_iterator >]': pdb2pka/pMC_mult_wrap.cpp:4314:22: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::distance(current, iters->get_current()); ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/8/bits/stl_algobase.h:66, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /usr/include/c++/8/stdexcept:39, from pdb2pka/pMC_mult_wrap.cpp:3075: /usr/include/c++/8/bits/stl_iterator_base_funcs.h: In function 'typename std::iterator_traits<_Iterator>::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 distance(_InputIterator __first, _InputIterator __last) ^~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/8/bits/stl_iterator_base_funcs.h:141:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 return std::__distance(__first, __last, ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ std::__iterator_category(__first)); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_funcs.h: In function 'constexpr typename std::iterator_traits<_Iterator>::difference_type std::__distance(_RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >]': /usr/include/c++/8/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 __distance(_RandomAccessIterator __first, _RandomAccessIterator __last, ^~~~~~~~~~ /usr/include/c++/8/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 g++ -o pdb2pka/_pMC_mult.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/pMC_mult.os pdb2pka/pMC_mult_wrap.os -L/usr/lib -lpython2.7 scons: done building targets. TARGETS: ['pdb2pqr.py', 'apbs_cgi.cgi', 'visualize.cgi', 'querystatus.cgi', 'src/aconf.py', 'html/server.html', 'pdb2pqr.cgi', 'pdb2pka/substruct/Algorithms.so', 'pdb2pka/_pMC_mult.so'] ======================== Configuration Parameters ======================== Version: 2.1.1 Install directory: /usr/share/pdb2pqr/ pdb2pka and ligand support: True Path to the website directory: http://localhost/pdb2pqr/ PDB2PQR jobs run via the web interface will be forked on the server. The preferred way to configure the build is by editing the file build_config.py Run scons with the python that you intend to use with pdb2pqr. For example: "/opt/bin/python scons/scons.py" will setup pdb2pqr to be run with /opt/bin/python Run "python scons/scons.py install" to install pdb2pqr in /usr/share/pdb2pqr/ Run "python scons/scons.py basic-test" for a basic functionality test Run "python scons/scons.py advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled. Run "python scons/scons.py complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled. Run "python scons/scons.py pdb2pka-test" for a test of PDB2PKA functionality. Requires numpy, PDB2PKA support compiled AND the APBS python libraries compiled and installed in the pdb2pka directory. To setup a web service create a symbolic link to /usr/share/pdb2pqr/ that enables you to view http://localhost/pdb2pqr/ after running "scons/scons.py install" Run "python scons/scons.py msvs" to build Visual Studio projects for the Algorithms and pMC_mult modules. VS project generation is not well supported in scons. Resulting projects should build using NMAKE but cannot be used for debugging. The resulting projects will need to modified to use VS natively to compile the code or debug. Build succeeded. make[1]: Leaving directory '/build/pdb2pqr-2.1.1+dfsg' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python2 dh_testroot dh_prep dh_installdirs debian/rules override_dh_install-arch make[1]: Entering directory '/build/pdb2pqr-2.1.1+dfsg' dh_install -a dos2unix debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py to Unix format... dos2unix debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py to Unix format... make[1]: Leaving directory '/build/pdb2pqr-2.1.1+dfsg' dh_install -Npdb2pqr dh_installdocs debian/rules override_dh_installchangelogs make[1]: Entering directory '/build/pdb2pqr-2.1.1+dfsg' dh_installchangelogs ChangeLog.md make[1]: Leaving directory '/build/pdb2pqr-2.1.1+dfsg' dh_installexamples debian/rules override_dh_installman-arch make[1]: Entering directory '/build/pdb2pqr-2.1.1+dfsg' dh_installman -a xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml Note: Writing pdb2pqr.1 xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml Note: Writing psize.1 xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/propka.1.xml Note: Writing propka.1 make[1]: Leaving directory '/build/pdb2pqr-2.1.1+dfsg' dh_python2 I: dh_python2 tools:114: replacing shebang in debian/pdb2pqr/usr/share/pdb2pqr/pdb2pqr.py dh_perl dh_link dh_strip_nondeterminism dh_compress debian/rules override_dh_fixperms-arch make[1]: Entering directory '/build/pdb2pqr-2.1.1+dfsg' dh_fixperms -a chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/main_cgi.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pka_routines.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py chmod 0644 debian/pdb2pqr/usr/share/pdb2pqr/src/errors.py chmod +x debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py chmod +x debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py make[1]: Leaving directory '/build/pdb2pqr-2.1.1+dfsg' dh_fixperms -Npdb2pqr dh_missing dh_strip dh_makeshlibs dh_shlibdeps dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'pdb2pqr-doc' in '../pdb2pqr-doc_2.1.1+dfsg-5_all.deb'. dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-5_armhf.deb'. dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-5_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../pdb2pqr_2.1.1+dfsg-5_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: user script /srv/workspace/pbuilder/29518/tmp/hooks/B01_cleanup starting I: user script /srv/workspace/pbuilder/29518/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/29518 and its subdirectories I: Current time: Sun Jun 7 00:09:48 +14 2020 I: pbuilder-time-stamp: 1591438188