pdb2pqr →
2.1.1+dfsg-5+b1 →
armhf → 2020-01-21 11:22:29
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| pdb2pqr 2.1.1+dfsg-5+b1 (armhf) Tue, 21 Jan 2020 11:00:29 +0000 |
+==============================================================================+
Package: pdb2pqr
Version: 2.1.1+dfsg-5+b1
Source Version: 2.1.1+dfsg-5
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-c399886b-1eaa-4a2b-99fd-002fc822fbda' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.3 MB in 26s (934 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pdb2pqr' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pdb2pqr.git
Please use:
git clone https://salsa.debian.org/med-team/pdb2pqr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5207 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-5 (dsc) [2277 B]
Get:2 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-5 (tar) [5191 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-5 (diff) [13.5 kB]
Fetched 5207 kB in 1s (7742 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pdb2pqr-IU0zcn/pdb2pqr-2.1.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-IU0zcn' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-6R04Uw/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-6R04Uw/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-6R04Uw/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ Packages [430 B]
Fetched 2106 B in 1s (2749 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 2 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (0 B/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12207 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: debhelper (>= 11~), dh-python, gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix
Filtered Build-Depends: debhelper (>= 11~), dh-python, gfortran, swig, xmlto, openbabel, python-dev, python-numpy, scons, dos2unix
dpkg-deb: building package 'sbuild-build-depends-pdb2pqr-dummy' in '/<<BUILDDIR>>/resolver-6R04Uw/apt_archive/sbuild-build-depends-pdb2pqr-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-pdb2pqr-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ Sources [543 B]
Get:5 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ Packages [624 B]
Fetched 2500 B in 1s (3304 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pdb2pqr build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism docbook-xml docbook-xsl
dos2unix dwz file fontconfig-config fonts-dejavu-core gettext gettext-base
gfortran gfortran-9 groff-base intltool-debian libarchive-zip-perl libblas3
libbsd0 libcairo2 libcroco3 libdebhelper-perl libelf1 libexpat1
libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-9-dev libgfortran5 libglib2.0-0 libicu63 liblapack3 libmagic-mgc
libmagic1 libmpdec2 libopenbabel5 libpipeline1 libpixman-1-0 libpng16-16
libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib libsigsegv2 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libx11-6 libx11-data
libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2
libxml2-utils libxrender1 libxslt1.1 m4 man-db mime-support openbabel
po-debconf python python-dev python-minimal python-numpy
python-pkg-resources python2 python2-dev python2-minimal python2.7
python2.7-dev python2.7-minimal python3 python3-distutils python3-lib2to3
python3-minimal python3.7 python3.7-minimal scons sensible-utils sgml-base
sgml-data swig swig3.0 ucf xml-core xmlto xsltproc
Suggested packages:
autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois
vacation dh-make docbook docbook-dsssl docbook-defguide dbtoepub
docbook-xsl-doc-html | docbook-xsl-doc-pdf | docbook-xsl-doc-text
| docbook-xsl-doc docbook-xsl-saxon fop libsaxon-java libxalan2-java
libxslthl-java xalan gettext-doc libasprintf-dev libgettextpo-dev
gfortran-doc gfortran-9-doc libcoarrays-dev groff libtool-doc gcj-jdk m4-doc
apparmor less www-browser libmail-box-perl python-doc python-tk
python-pytest python-numpy-dbg python-numpy-doc python-setuptools
python2-doc python2.7-doc binfmt-support python3-doc python3-tk python3-venv
python3.7-venv python3.7-doc sgml-base-doc perlsgml w3-recs opensp swig-doc
swig-examples swig3.0-examples swig3.0-doc w3m | lynx-cur | links
texlive-htmlxml
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl dblatex | fop libpaper-utils
zip
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-python dh-strip-nondeterminism docbook-xml docbook-xsl
dos2unix dwz file fontconfig-config fonts-dejavu-core gettext gettext-base
gfortran gfortran-9 groff-base intltool-debian libarchive-zip-perl libblas3
libbsd0 libcairo2 libcroco3 libdebhelper-perl libelf1 libexpat1
libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-9-dev libgfortran5 libglib2.0-0 libicu63 liblapack3 libmagic-mgc
libmagic1 libmpdec2 libopenbabel5 libpipeline1 libpixman-1-0 libpng16-16
libpython-dev libpython-stdlib libpython2-dev libpython2-stdlib libpython2.7
libpython2.7-dev libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib libsigsegv2 libssl1.1
libsub-override-perl libtinfo5 libtool libuchardet0 libx11-6 libx11-data
libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2
libxml2-utils libxrender1 libxslt1.1 m4 man-db mime-support openbabel
po-debconf python python-dev python-minimal python-numpy
python-pkg-resources python2 python2-dev python2-minimal python2.7
python2.7-dev python2.7-minimal python3 python3-distutils python3-lib2to3
python3-minimal python3.7 python3.7-minimal
sbuild-build-depends-pdb2pqr-dummy scons sensible-utils sgml-base sgml-data
swig swig3.0 ucf xml-core xmlto xsltproc
0 upgraded, 108 newly installed, 0 to remove and 2 not upgraded.
Need to get 80.8 MB of archives.
After this operation, 252 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-6R04Uw/apt_archive ./ sbuild-build-depends-pdb2pqr-dummy 0.invalid.0 [912 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.1+20191019-1 [316 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [783 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.2-2 [29.6 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.0-2 [1261 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-minimal armhf 2.7.17-1 [395 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf python2.7-minimal armhf 2.7.17-1 [1107 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf python2-minimal armhf 2.7.17-2 [41.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python-minimal armhf 2.7.17-2 [21.1 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.64 [37.8 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-stdlib armhf 2.7.17-1 [1823 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python2.7 armhf 2.7.17-1 [309 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython2-stdlib armhf 2.7.17-2 [20.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libpython-stdlib armhf 2.7.17-2 [20.9 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf python2 armhf 2.7.17-2 [41.7 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python armhf 2.7.17-2 [22.9 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.6-1 [585 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.6-1 [1527 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.7.5-3 [36.8 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmpdec2 armhf 2.4.2-2 [67.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.6-1 [1669 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.6-1 [350 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.7.5-3 [20.2 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.7.5-3 [62.1 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf sgml-base all 1.29.1 [15.0 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-3 [262 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-3 [112 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-3 [66.8 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11 [341 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-11 [547 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.7.3 [174 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.67-1 [104 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-1 [23.6 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-1 [14.6 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.62.4-1 [1138 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-2 [7974 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.4+dfsg1-8 [593 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.7.3 [1019 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.0-1 [78.3 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.0-1 [145 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20191017 [94.4 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf sgml-data all 2.0.11 [179 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf docbook-xml all 4.5-9 [84.4 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf docbook-xsl all 1.79.1+dfsg-2 [1249 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf dos2unix armhf 7.4.0-2 [386 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 9.2.1-22+rpi1 [230 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.2.1-22+rpi1 [279 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.2.1-22+rpi1 [8092 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-1 [274 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.1-2 [330 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-2 [132 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.8-1 [298 kB]
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Get:84 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.13.1-2 [108 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.13.1-2 [99.3 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.9-1 [119 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libopenbabel5 armhf 2.4.1+dfsg-6 [2592 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7 armhf 2.7.17-1 [883 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libpython2.7-dev armhf 2.7.17-1 [26.5 MB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libpython2-dev armhf 2.7.17-2 [21.0 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpython-dev armhf 2.7.17-2 [21.0 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libxml2-utils armhf 2.9.4+dfsg1-8 [96.1 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libxslt1.1 armhf 1.1.32-2.2 [215 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf openbabel armhf 2.4.1+dfsg-6 [119 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf python2.7-dev armhf 2.7.17-1 [284 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf python2-dev armhf 2.7.17-2 [1224 B]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf python-dev armhf 2.7.17-2 [1196 B]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf python-pkg-resources all 44.0.0-1 [184 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf python-numpy armhf 1:1.16.5-3 [1919 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf scons all 3.1.1-3 [561 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf swig3.0 armhf 3.0.12-2.2 [1242 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf swig armhf 3.0.12-2.2 [310 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf xsltproc armhf 1.1.32-2.2 [121 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf xmlto armhf 0.0.28-2.1 [32.1 kB]
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Setting up libpython2.7-stdlib:armhf (2.7.17-1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libexpat1-dev:armhf (2.2.9-1) ...
Setting up swig3.0 (3.0.12-2.2) ...
Setting up libx11-data (2:1.6.8-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libpng16-16:armhf (1.6.37-1) ...
Setting up autopoint (0.19.8.1-10) ...
Setting up fonts-dejavu-core (2.37-1) ...
Setting up libgfortran5:armhf (9.2.1-22+rpi1) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up sgml-base (1.29.1) ...
Setting up dos2unix (7.4.0-2) ...
Setting up libmpdec2:armhf (2.4.2-2) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.1+20191019-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.4+dfsg1-8) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libpython3.7-stdlib:armhf (3.7.6-1) ...
Setting up libpython2.7:armhf (2.7.17-1) ...
Setting up liblapack3:armhf (3.9.0-1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libpython2.7-dev:armhf (2.7.17-1) ...
Setting up libxcb1:armhf (1.13.1-2) ...
Setting up swig (3.0.12-2.2) ...
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Setting up libtool (2.4.6-11) ...
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Setting up m4 (1.4.18-4) ...
Setting up libxcb-shm0:armhf (1.13.1-2) ...
Setting up python2 (2.7.17-2) ...
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Setting up libfreetype6:armhf (2.10.1-2) ...
Setting up bsdmainutils (11.1.2) ...
update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode
update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up autoconf (2.69-11) ...
Setting up dh-strip-nondeterminism (1.6.3-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-4) ...
Setting up xml-core (0.18+nmu1) ...
Setting up libxslt1.1:armhf (1.1.32-2.2) ...
Setting up libx11-6:armhf (2:1.6.8-1) ...
Setting up libpython2-dev:armhf (2.7.17-2) ...
Setting up libxml2-utils (2.9.4+dfsg1-8) ...
Setting up python (2.7.17-2) ...
Setting up libpython3-stdlib:armhf (3.7.5-3) ...
Setting up python2.7-dev (2.7.17-1) ...
Setting up automake (1:1.16.1-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up python3.7 (3.7.6-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up python2-dev (2.7.17-2) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up gfortran-9 (9.2.1-22+rpi1) ...
Setting up python-pkg-resources (44.0.0-1) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up xsltproc (1.1.32-2.2) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up python3 (3.7.5-3) ...
Setting up man-db (2.9.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:9.2.1-3.1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libpython-dev:armhf (2.7.17-2) ...
Setting up scons (3.1.1-3) ...
Setting up libfontconfig1:armhf (2.13.1-2) ...
Setting up python3-lib2to3 (3.8.0-1) ...
Setting up python-dev (2.7.17-2) ...
Setting up python3-distutils (3.8.0-1) ...
Setting up dh-python (4.20191017) ...
Setting up python-numpy (1:1.16.5-3) ...
Setting up po-debconf (1.0.21) ...
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up libopenbabel5 (2.4.1+dfsg-6) ...
Setting up openbabel (2.4.1+dfsg-6) ...
Setting up debhelper (12.7.3) ...
Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.29-7+rpi1) ...
Processing triggers for sgml-base (1.29.1) ...
Setting up docbook-xsl (1.79.1+dfsg-2) ...
Setting up sgml-data (2.0.11) ...
Processing triggers for sgml-base (1.29.1) ...
Setting up docbook-xml (4.5-9) ...
Processing triggers for sgml-base (1.29.1) ...
Setting up xmlto (0.0.28-2.1) ...
Setting up sbuild-build-depends-pdb2pqr-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.2-armmp armhf (armv7l)
Toolchain package versions: binutils_2.33.1-6+rpi1 dpkg-dev_1.19.7 g++-9_9.2.1-22+rpi1 gcc-9_9.2.1-22+rpi1 libc6-dev_2.29-7+rpi1 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.47 bash_5.0-5 binutils_2.33.1-6+rpi1 binutils-arm-linux-gnueabihf_2.33.1-6+rpi1 binutils-common_2.33.1-6+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.2.1-22+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.7.3 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20191017 dh-strip-nondeterminism_1.6.3-1 diffutils_1:3.7-3 dirmngr_2.2.19-1 docbook-xml_4.5-9 docbook-xsl_1.79.1+dfsg-2 dos2unix_7.4.0-2 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-3 findutils_4.7.0-1 fontconfig-config_2.13.1-2 fonts-dejavu-core_2.37-1 g++_4:9.2.1-3.1+rpi1 g++-9_9.2.1-22+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-9_9.2.1-22+rpi1 gcc-9-base_9.2.1-22+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.2.1-22+rpi1 gnupg_2.2.19-1 gnupg-l10n_2.2.19-1 gnupg-utils_2.2.19-1 gpg_2.2.19-1 gpg-agent_2.2.19-1 gpg-wks-client_2.2.19-1 gpg-wks-server_2.2.19-1 gpgconf_2.2.19-1 gpgsm_2.2.19-1 gpgv_2.2.19-1 grep_3.3-1 groff-base_1.22.4-4 gzip_1.9-3 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20190709-2 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-22+rpi1 libassuan0_2.5.3-7 libatomic1_9.2.1-22+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.33.1-6+rpi1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-7+rpi1 libc-dev-bin_2.29-7+rpi1 libc6_2.29-7+rpi1 libc6-dev_2.29-7+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.1 libcap2_1:2.27-1 libcap2-bin_1:2.27-1 libcc1-0_9.2.1-22+rpi1 libcom-err2_1.45.5-2 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10+b5 libcrypt1_1:4.4.10-10+b5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.250 libdebhelper-perl_12.7.3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libfile-stripnondeterminism-perl_1.6.3-1 libfontconfig1_2.13.1-2 libfreetype6_2.10.1-2 libgcc-9-dev_9.2.1-22+rpi1 libgcc1_1:9.2.1-22+rpi1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.2.1-22+rpi1 libgfortran5_9.2.1-22+rpi1 libglib2.0-0_2.62.4-1 libgmp10_2:6.1.2+dfsg-4 libgnutls30_3.6.11.1-2 libgomp1_9.2.1-22+rpi1 libgpg-error0_1.36-7 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libisl22_0.22-2 libksba8_1.3.5-2 liblapack3_3.9.0-1 libldap-2.4-2_2.4.48+dfsg-1+b2 libldap-common_2.4.48+dfsg-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-3 libmagic1_1:5.38-3 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libncursesw6_6.1+20191019-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libopenbabel5_2.4.1+dfsg-6 libp11-kit0_0.23.18.1-2 libpam-cap_1:2.27-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpixman-1-0_0.36.0-1 libpng16-16_1.6.37-1 libpython-dev_2.7.17-2 libpython-stdlib_2.7.17-2 libpython2-dev_2.7.17-2 libpython2-stdlib_2.7.17-2 libpython2.7_2.7.17-1 libpython2.7-dev_2.7.17-1 libpython2.7-minimal_2.7.17-1 libpython2.7-stdlib_2.7.17-1 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1 libpython3.7-stdlib_3.7.6-1 libreadline7_7.0-5 libreadline8_8.0-3 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.2-2+rpi1 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.30.1+fossil191229-1 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-22+rpi1 libstdc++6_9.2.1-22+rpi1 libsub-override-perl_0.09-2 libsystemd0_244-3+rpi1+b1 libtasn1-6_4.15.0-2 libtinfo5_6.1+20191019-1 libtinfo6_6.1+20191019-1 libtool_2.4.6-11 libubsan1_9.2.1-22+rpi1 libuchardet0_0.0.6-3 libudev1_244-3+rpi1+b1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libx11-6_2:1.6.8-1 libx11-data_2:1.6.8-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-2 libxcb-shm0_1.13.1-2 libxcb1_1.13.1-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.4+dfsg1-8 libxml2-utils_2.9.4+dfsg1-8 libxrender1_1:0.9.10-1 libxslt1.1_1.1.32-2.2 libzstd1_1.4.4+dfsg-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8-1 logsave_1.45.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.3-17 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 netbase_6.0 openbabel_2.4.1+dfsg-6 passwd_1:4.8-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 pinentry-curses_1.1.0-3 po-debconf_1.0.21 python_2.7.17-2 python-dev_2.7.17-2 python-minimal_2.7.17-2 python-numpy_1:1.16.5-3 python-pkg-resources_44.0.0-1 python2_2.7.17-2 python2-dev_2.7.17-2 python2-minimal_2.7.17-2 python2.7_2.7.17-1 python2.7-dev_2.7.17-1 python2.7-minimal_2.7.17-1 python3_3.7.5-3 python3-distutils_3.8.0-1 python3-lib2to3_3.8.0-1 python3-minimal_3.7.5-3 python3.7_3.7.6-1 python3.7-minimal_3.7.6-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-3 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pdb2pqr-dummy_0.invalid.0 scons_3.1.1-3 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.29.1 sgml-data_2.0.11 swig_3.0.12-2.2 swig3.0_3.0.12-2.2 sysvinit-utils_2.96-1 tar_1.30+dfsg-6 tzdata_2019c-3 ucf_3.0038+nmu1 util-linux_2.34-0.1 xml-core_0.18+nmu1 xmlto_0.0.28-2.1 xsltproc_1.1.32-2.2 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-1
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Mon May 27 06:43:35 2019 UTC
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 /<<BUILDDIR>>/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
Check disc space
----------------
Sufficient free space for build
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.1.1+dfsg-5+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-c399886b-1eaa-4a2b-99fd-002fc822fbda
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pdb2pqr
dpkg-buildpackage: info: source version 2.1.1+dfsg-5+b1
dpkg-buildpackage: info: source distribution bullseye-staging
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 '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_clean
debian/rules build-arch
dh build-arch --with python2
dh_update_autotools_config -a
dh_autoreconf -a
debian/rules override_dh_auto_configure
make[1]: Entering directory '/<<BUILDDIR>>/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]
17 | #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++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:555:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
555 | std::__uninitialized_copy_a(__x.begin(), __x.end(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
556 | this->_M_impl._M_start,
| ~~~~~~~~~~~~~~~~~~~~~~~
557 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
305 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
307 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:121:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]':
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
115 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
137 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
138 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
139 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
140 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/stl_uninitialized.h:329:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
328 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]':
/usr/include/c++/9/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
99 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
101 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
305 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
307 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
465 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algobase.h:474:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
473 | return std::__copy_move_a2<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
474 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
115 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
137 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
138 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
139 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
140 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:61,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/9/bits/cpp_type_traits.h:428:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
428 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
438 | __copy_move_a2(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/9/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
99 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
101 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:67,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector<double>]':
/usr/include/c++/9/bits/stl_iterator.h:1010:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1010 | __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
465 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algobase.h:67,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/9/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++/9/bits/stl_iterator.h:1262:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
1262 | __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<double>::iterator std_vector_Sl_double_Sg__erase__SWIG_0(std::vector<double>*, std::vector<double>::iterator)':
pdb2pka/pMC_mult_wrap.cpp:5089:44: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
5089 | 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<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
5089 | 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<double>::iterator std_vector_Sl_double_Sg__erase__SWIG_1(std::vector<double>*, std::vector<double>::iterator, std::vector<double>::iterator)':
pdb2pka/pMC_mult_wrap.cpp:5090:44: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
5090 | 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<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp:5090:218: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
5090 | 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<double>::iterator std_vector_Sl_double_Sg__insert__SWIG_0(std::vector<double>*, std::vector<double>::iterator, const value_type&)':
pdb2pka/pMC_mult_wrap.cpp:5091:44: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
5091 | 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<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
5091 | 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<double>*, std::vector<double>::iterator, std::vector<double>::size_type, const value_type&)':
pdb2pka/pMC_mult_wrap.cpp:5092:17: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
5092 | 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<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
5092 | 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<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
9290 | 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<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
9343 | 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<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
9753 | 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<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
9810 | std_vector_Sl_double_Sg__insert__SWIG_1(arg1,arg2,arg3,(double const &)*arg4);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_vector.h: In copy constructor 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:555:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
555 | std::__uninitialized_copy_a(__x.begin(), __x.end(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
556 | this->_M_impl._M_start,
| ~~~~~~~~~~~~~~~~~~~~~~~
557 | _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<double*, std::vector<double> >]':
pdb2pka/pMC_mult_wrap.cpp:4441:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4441 | return new SwigPyIteratorClosed_T<OutIter>(current, begin, end, seq);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4441:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' 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<double>; Difference = int]':
pdb2pka/pMC_mult_wrap.cpp:4106:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
4106 | 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<double>; Difference = int; InputSeq = std::vector<double>]':
pdb2pka/pMC_mult_wrap.cpp:4152:33: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4152 | 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<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4152 | 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<const double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp:4159:11: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4159 | self->erase(sb,se);
| ^~~~
pdb2pka/pMC_mult_wrap.cpp:4162:11: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4162 | 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<const double*, std::vector<double> >' 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<double>; Difference = int]':
pdb2pka/pMC_mult_wrap.cpp:4211:9: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4211 | self->erase(sb,se);
| ^~~~
pdb2pka/pMC_mult_wrap.cpp:4216:14: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4216 | it = self->erase(it);
pdb2pka/pMC_mult_wrap.cpp:4228:9: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4228 | 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<double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::erase(Sequence*, const typename Sequence::iterator&) [with Sequence = std::vector<double>]':
pdb2pka/pMC_mult_wrap.cpp:4082:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4082 | seq->erase(position);
| ^~~
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_vector.h: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:1195:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1195 | _M_realloc_insert(end(), __x);
| ^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(std::vector<_Tp, _Alloc>::const_iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:1427:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
1427 | erase(const_iterator __position)
| ^~~~~
/usr/include/c++/9/bits/stl_vector.h:1428:58: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1428 | { return _M_erase(begin() + (__position - cbegin())); }
| ^
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/stl_vector.h:1454:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
1454 | erase(const_iterator __first, const_iterator __last)
| ^~~~~
/usr/include/c++/9/bits/stl_vector.h:1454:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1458:71: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1458 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
| ^
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/vector.tcc:130:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
130 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:154:6: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
154 | _M_insert_aux(__pos, std::move(__x_copy._M_val()));
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:161:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/stl_vector.h:1332:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
1332 | insert(const_iterator __position, size_type __n, const value_type& __x)
| ^~~~~~
/usr/include/c++/9/bits/stl_vector.h:1335:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1335 | _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<double*, std::vector<double> >]':
pdb2pka/pMC_mult_wrap.cpp:4448:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4448 | return new SwigPyIteratorOpen_T<OutIter>(current, seq);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::reverse_iterator std::vector<_Tp, _Alloc>::rbegin() [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:845:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
845 | { return reverse_iterator(end()); }
| ^
/usr/include/c++/9/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::reverse_iterator std::vector<_Tp, _Alloc>::rend() [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:863:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
863 | { return reverse_iterator(begin()); }
| ^
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/stl_vector.h:957:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
957 | _M_fill_insert(end(), __new_size - size(), __x);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::reserve(std::vector<_Tp, _Alloc>::size_type) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:85:14: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
85 | __tmp = _M_allocate_and_copy(__n,
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/vector.tcc:226:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
226 | pointer __tmp = _M_allocate_and_copy(__xlen, __x.begin(),
| ^~~~~
/usr/include/c++/9/bits/vector.tcc:238:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
238 | std::_Destroy(std::copy(__x.begin(), __x.end(), begin()),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
239 | end(), _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:238:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
305 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
307 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIteratorClosed_T<OutIterator, ValueType, FromOper>::SwigPyIteratorClosed_T(swig::SwigPyIteratorClosed_T<OutIterator, ValueType, FromOper>::out_iterator, swig::SwigPyIteratorClosed_T<OutIterator, ValueType, FromOper>::out_iterator, swig::SwigPyIteratorClosed_T<OutIterator, ValueType, FromOper>::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; ValueType = double; FromOper = swig::from_oper<double>]':
pdb2pka/pMC_mult_wrap.cpp:4390:5: note: parameter passing for argument of type 'swig::SwigPyIteratorClosed_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
4390 | 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*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} 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*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} 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*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
4391 | : SwigPyIterator_T<OutIterator>(curr, seq), begin(first), end(last)
| ^
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; <template-parameter-2-2> = void; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:650:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
650 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/9/bits/stl_vector.h:650:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:654:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
654 | _M_range_initialize(__first, __last,
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/stl_vector.h:854:44: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
854 | { return const_reverse_iterator(end()); }
| ^
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
465 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algobase.h:474:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
473 | return std::__copy_move_a2<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
474 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<const double*, std::vector<double> >; <template-parameter-2-2> = void; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:1376:2: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
1376 | insert(const_iterator __position, _InputIterator __first,
| ^~~~~~
/usr/include/c++/9/bits/stl_vector.h:1376:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1376:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1380:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1380 | _M_insert_dispatch(begin() + __offset,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1380:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/stl_algobase.h:67,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_iterator.h: In constructor 'std::reverse_iterator<_Iterator>::reverse_iterator(std::reverse_iterator<_Iterator>::iterator_type) [with _Iterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_iterator.h:137:7: note: parameter passing for argument of type 'std::reverse_iterator<__gnu_cxx::__normal_iterator<double*, std::vector<double> > >::iterator_type' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
137 | reverse_iterator(iterator_type __x) : current(__x) { }
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/vector.tcc:175:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
175 | _GLIBCXX_MOVE3(__position + 1, end(), __position);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
184 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:184:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/vector.tcc:190:6: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
190 | _GLIBCXX_MOVE3(__last, end(), __first);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/vector.tcc:395:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
395 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIteratorOpen_T<OutIterator, ValueType, FromOper>::SwigPyIteratorOpen_T(swig::SwigPyIteratorOpen_T<OutIterator, ValueType, FromOper>::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; ValueType = double; FromOper = swig::from_oper<double>]':
pdb2pka/pMC_mult_wrap.cpp:4347:5: note: parameter passing for argument of type 'swig::SwigPyIteratorOpen_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
4347 | 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*, std::vector<double> >, double, swig::from_oper<double> >::out_iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
4348 | : SwigPyIterator_T<OutIterator>(curr, seq)
| ^
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/vector.tcc:267:13: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
267 | std::fill(begin(), end(), __val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double*>; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:1505:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
1505 | _M_allocate_and_copy(size_type __n,
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1505:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1511:35: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
1511 | std::__uninitialized_copy_a(__first, __last, __result,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1512 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:1505:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1505 | _M_allocate_and_copy(size_type __n,
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1505:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1511:35: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1511 | std::__uninitialized_copy_a(__first, __last, __result,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1512 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:65,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator, std::allocator<_T2>&) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double]':
/usr/include/c++/9/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
203 | _Destroy(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~
/usr/include/c++/9/bits/stl_construct.h:203:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_construct.h:206:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
206 | _Destroy(__first, __last);
| ~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]':
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
115 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
137 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
138 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
139 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
140 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyIterator_T<OutIterator>::SwigPyIterator_T(swig::SwigPyIterator_T<OutIterator>::out_iterator, PyObject*) [with OutIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
pdb2pka/pMC_mult_wrap.cpp:4289:5: note: parameter passing for argument of type 'swig::SwigPyIterator_T<__gnu_cxx::__normal_iterator<double*, std::vector<double> > >::out_iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
4289 | SwigPyIterator_T(out_iterator curr, PyObject *seq)
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:1574:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1574 | _M_range_initialize(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1574:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1577:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1577 | const size_type __n = std::distance(__first, __last);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1582:33: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1582 | std::__uninitialized_copy_a(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1583 | this->_M_impl._M_start,
| ~~~~~~~~~~~~~~~~~~~~~~~
1584 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:67,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_iterator.h: In constructor 'std::reverse_iterator<_Iterator>::reverse_iterator(std::reverse_iterator<_Iterator>::iterator_type) [with _Iterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_iterator.h:137:7: note: parameter passing for argument of type 'std::reverse_iterator<__gnu_cxx::__normal_iterator<const double*, std::vector<double> > >::iterator_type' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
137 | reverse_iterator(iterator_type __x) : current(__x) { }
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/cmath:42,
from /usr/include/c++/9/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++/9/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/9/bits/cpp_type_traits.h:428:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
428 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
438 | __copy_move_a2(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/stl_vector.h:1659:2: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
1659 | _M_insert_dispatch(iterator __pos, _InputIterator __first,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1659:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1659:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
1662 | _M_range_insert(__pos, __first, __last,
| ^~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_vector.h:1662:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/stl_uninitialized.h:329:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
328 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
330 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::move(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _OI = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_algobase.h:497:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
497 | move(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/9/bits/stl_algobase.h:497:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algobase.h:497:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algobase.h:505:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
505 | return std::__copy_move_a2<true>(std::__miter_base(__first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
506 | std::__miter_base(__last), __result);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_move_a(_InputIterator, _InputIterator, _ForwardIterator, _Allocator&) [with _InputIterator = double*; _ForwardIterator = double*; _Allocator = std::allocator<double>]':
/usr/include/c++/9/bits/stl_uninitialized.h:315:41: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
315 | return std::__uninitialized_copy_a(_GLIBCXX_MAKE_MOVE_ITERATOR(__first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
316 | _GLIBCXX_MAKE_MOVE_ITERATOR(__last),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
317 | __result, __alloc);
| ~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function 'void std::fill(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double]':
/usr/include/c++/9/bits/stl_algobase.h:742:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
742 | fill(_ForwardIterator __first, _ForwardIterator __last, const _Tp& __value)
| ^~~~
/usr/include/c++/9/bits/stl_algobase.h:742:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*; _Tp = double]':
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
305 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:305:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:307:37: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
307 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:65,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_construct.h:127:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
127 | _Destroy(_ForwardIterator __first, _ForwardIterator __last)
| ^~~~~~~~
/usr/include/c++/9/bits/stl_construct.h:127:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_construct.h:137:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
136 | std::_Destroy_aux<__has_trivial_destructor(_Value_type)>::
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
137 | __destroy(__first, __last);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _ForwardIterator = double*]':
/usr/include/c++/9/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
99 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
101 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:66,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/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<const double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
138 | distance(_InputIterator __first, _InputIterator __last)
| ^~~~~~~~
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:141:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
141 | return std::__distance(__first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
142 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:67,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = const double*; _Container = std::vector<double>]':
/usr/include/c++/9/bits/stl_iterator.h:1010:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1010 | __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
| ^~~~~~~~~~~~
/usr/include/c++/9/bits/stl_iterator.h: In function '_Iterator std::__niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container>) [with _Iterator = double*; _Container = std::vector<double>]':
/usr/include/c++/9/bits/stl_iterator.h:1010:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function '_From std::__niter_wrap(_From, _To) [with _From = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _To = double*]':
/usr/include/c++/9/bits/stl_algobase.h:289:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
289 | __niter_wrap(_From __from, _To __res)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<const double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/vector.tcc:727:41: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
727 | const size_type __n = std::distance(__first, __last);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:744:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
744 | std::copy(__first, __last, __position);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:751:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
751 | std::__uninitialized_copy_a(__mid, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
752 | this->_M_impl._M_finish,
| ~~~~~~~~~~~~~~~~~~~~~~~~
753 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:762:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
762 | std::copy(__first, __mid, __position);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:778:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
778 | = std::__uninitialized_copy_a(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
779 | __new_finish,
| ~~~~~~~~~~~~~
780 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/cmath:42,
from /usr/include/c++/9/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++/9/bits/cpp_type_traits.h: In function '_Iterator std::__miter_base(_Iterator) [with _Iterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/9/bits/cpp_type_traits.h:428:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
428 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = true; _II = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _OI = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
438 | __copy_move_a2(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::assign(const SwigPySeq&, Seq*) [with SwigPySeq = swig::SwigPySequence_Cont<double>; Seq = std::vector<double>]':
pdb2pka/pMC_mult_wrap.cpp:4739:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
4739 | seq->insert(seq->end(),(value_type)(*it));
| ^~~
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
115 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:115:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:140:15: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
137 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
138 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
139 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
140 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/vector:65,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_construct.h: In static member function 'static void std::_Destroy_aux<true>::__destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_construct.h:117:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
117 | __destroy(_ForwardIterator, _ForwardIterator) { }
| ^~~~~~~~~
/usr/include/c++/9/bits/stl_construct.h:117:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
465 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_algobase.h:474:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
473 | return std::__copy_move_a2<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
474 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:66,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/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<const double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
98 | __distance(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/stl_vector.h:1290:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
1290 | insert(const_iterator __position, value_type&& __x)
| ^~~~~~
/usr/include/c++/9/bits/stl_vector.h:1291:57: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
1291 | { return _M_insert_rval(__position, std::move(__x)); }
| ^
In file included from /usr/include/c++/9/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/stl_uninitialized.h: In static member function 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/9/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
99 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_uninitialized.h:99:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/9/bits/stl_uninitialized.h:101:27: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
101 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
438 | __copy_move_a2(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~~
/usr/include/c++/9/bits/stl_algobase.h:438:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/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<double>]':
/usr/include/c++/9/bits/vector.tcc:340:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator' {aka '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >'} changed in GCC 7.1
340 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:354:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
354 | _M_insert_aux(begin() + __n, std::move(__v));
| ^~~~~~~~~~~~~
/usr/include/c++/9/bits/vector.tcc:356:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
356 | _M_realloc_insert(begin() + __n, std::move(__v));
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
465 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/9/bits/stl_algobase.h:465:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/9/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:3148:
/usr/include/c++/9/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/9/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' {aka '__gnu_cxx::__normal_iterator<double*, std::vector<double> >'} changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:67,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/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++/9/bits/stl_iterator.h:1262:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
1262 | __miter_base(move_iterator<_Iterator> __it)
| ^~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In member function 'ptrdiff_t swig::SwigPyIterator_T<OutIterator>::distance(const swig::SwigPyIterator&) const [with OutIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
pdb2pka/pMC_mult_wrap.cpp:4314:22: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4314 | return std::distance(current, iters->get_current());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/9/bits/stl_algobase.h:66,
from /usr/include/c++/9/bits/char_traits.h:39,
from /usr/include/c++/9/string:40,
from /usr/include/c++/9/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:3075:
/usr/include/c++/9/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<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
138 | distance(_InputIterator __first, _InputIterator __last)
| ^~~~~~~~
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:138:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:141:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
141 | return std::__distance(__first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
142 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/9/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<double*, std::vector<double> >]':
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
98 | __distance(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/9/bits/stl_iterator_base_funcs.h:98:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' 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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
create-stamp debian/debhelper-build-stamp
fakeroot debian/rules binary-arch
dh binary-arch --with python2
dh_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installchangelogs ChangeLog.md
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installexamples -a
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_python2 -a
I: dh_python2 tools:114: replacing shebang in debian/pdb2pqr/usr/share/pdb2pqr/pdb2pqr.py
dh_perl -a
dh_link -a
dh_strip_nondeterminism -a
dh_compress -a
debian/rules override_dh_fixperms-arch
make[1]: Entering directory '/<<BUILDDIR>>/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 '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_missing -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
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dh_builddeb -a
dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-5+b1_armhf.deb'.
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-5+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pdb2pqr_2.1.1+dfsg-5+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-01-21T11:22:23Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pdb2pqr_2.1.1+dfsg-5+b1_armhf.changes:
--------------------------------------
Format: 1.8
Date: Mon, 27 May 2019 01:52:46 -0400
Source: pdb2pqr (2.1.1+dfsg-5)
Binary: pdb2pqr pdb2pqr-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 2.1.1+dfsg-5+b1
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
pdb2pqr - Preparation of protein structures for electrostatics calculations
Changes:
pdb2pqr (2.1.1+dfsg-5+b1) bullseye-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pdb2pqr-dbgsym_2.1.1+dfsg-5+b1_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 336720 bytes: control archive=604 bytes.
442 bytes, 12 lines control
212 bytes, 2 lines md5sums
Package: pdb2pqr-dbgsym
Source: pdb2pqr (2.1.1+dfsg-5)
Version: 2.1.1+dfsg-5+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 549
Depends: pdb2pqr (= 2.1.1+dfsg-5+b1)
Section: debug
Priority: optional
Description: debug symbols for pdb2pqr
Build-Ids: 4a4f20733233ae01b007b35e6250d672c45d474b 86421f57ec4f7fa1ac452ec76055da4d7e20ef09
drwxr-xr-x root/root 0 2019-05-27 05:52 ./
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/debug/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/debug/.build-id/4a/
-rw-r--r-- root/root 34764 2019-05-27 05:52 ./usr/lib/debug/.build-id/4a/4f20733233ae01b007b35e6250d672c45d474b.debug
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/debug/.build-id/86/
-rw-r--r-- root/root 515664 2019-05-27 05:52 ./usr/lib/debug/.build-id/86/421f57ec4f7fa1ac452ec76055da4d7e20ef09.debug
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/share/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/share/doc/
lrwxrwxrwx root/root 0 2019-05-27 05:52 ./usr/share/doc/pdb2pqr-dbgsym -> pdb2pqr
pdb2pqr_2.1.1+dfsg-5+b1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 367792 bytes: control archive=4708 bytes.
1427 bytes, 29 lines control
9706 bytes, 131 lines md5sums
175 bytes, 9 lines * postinst #!/bin/sh
253 bytes, 14 lines * prerm #!/bin/sh
Package: pdb2pqr
Source: pdb2pqr (2.1.1+dfsg-5)
Version: 2.1.1+dfsg-5+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2834
Depends: libc6 (>= 2.29), libgcc1 (>= 1:3.5), libpython2.7 (>= 2.7), libstdc++6 (>= 5.2), python2:any, python-numpy, python-networkx
Suggests: apbs
Enhances: autodocktools
Replaces: propka
Provides: propka
Section: science
Priority: optional
Homepage: https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Description: Preparation of protein structures for electrostatics calculations
PDB2PQR is a Python software package that automates many of the common
tasks of preparing structures for continuum electrostatics calculations.
It thus provides a platform-independent utility for converting protein files
in PDB format to PQR format. These tasks include:
* Adding a limited number of missing heavy atoms to biomolecular structures
* Determining side-chain pKas
* Placing missing hydrogens
* Optimizing the protein for favorable hydrogen bonding
* Assigning charge and radius parameters from a variety of force fields
.
This package also includes PropKa, a tool to modify the protonation state of
protein structures in the Protein Data Bank (PDB) format to match a given pKa
value. It can also be used to refine NMR structures, which often yield
inaccurate pKa values for some residues.
drwxr-xr-x root/root 0 2019-05-27 05:52 ./
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/bin/
lrwxrwxrwx root/root 0 2019-05-27 05:52 ./usr/bin/pdb2pqr -> ../share/pdb2pqr/pdb2pqr.py
lrwxrwxrwx root/root 0 2019-05-27 05:52 ./usr/bin/propka -> ../share/pdb2pqr/propka30/propka.py
lrwxrwxrwx root/root 0 2019-05-27 05:52 ./usr/bin/psize -> ../share/pdb2pqr/src/psize.py
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/pdb2pqr/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/pdb2pqr/pdb2pka/
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drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/lib/pdb2pqr/pdb2pka/substruct/
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drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/share/pdb2pqr/extensions/
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drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/share/python/
drwxr-xr-x root/root 0 2019-05-27 05:52 ./usr/share/python/runtime.d/
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 54188
Build-Time: 109
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 1150
Job: pdb2pqr_2.1.1+dfsg-5
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 1314
Source-Version: 2.1.1+dfsg-5
Space: 54188
Status: successful
Version: 2.1.1+dfsg-5+b1
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Finished at 2020-01-21T11:22:23Z
Build needed 00:21:54, 54188k disc space