pdb2pqr →
2.1.1+dfsg-6 →
armhf → 2020-03-30 21:45:16
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-03
+==============================================================================+
| pdb2pqr 2.1.1+dfsg-6 (armhf) Mon, 30 Mar 2020 21:32:12 +0000 |
+==============================================================================+
Package: pdb2pqr
Version: 2.1.1+dfsg-6
Source Version: 2.1.1+dfsg-6
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-b2d8f63a-531c-4e09-9f29-cfecc97c2eb0' 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 [11.6 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.8 MB]
Fetched 24.4 MB in 25s (964 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 5261 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-6 (dsc) [2285 B]
Get:2 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-6 (tar) [5191 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-6 (diff) [67.2 kB]
Fetched 5261 kB in 0s (10.6 MB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pdb2pqr-GAhkbo/pdb2pqr-2.1.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-GAhkbo' 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-Q2SGA8/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-Q2SGA8/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-Q2SGA8/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-Q2SGA8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ Packages [431 B]
Fetched 2107 B in 1s (2860 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 1 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (13.5 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12230 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-compat (= 12), dh-python, gfortran, swig, xmlto, openbabel, python3-dev, python3-numpy, scons (>= 3.1.1-4), dos2unix, pkg-config
Filtered Build-Depends: debhelper-compat (= 12), dh-python, gfortran, swig, xmlto, openbabel, python3-dev, python3-numpy, scons (>= 3.1.1-4), dos2unix, pkg-config
dpkg-deb: building package 'sbuild-build-depends-pdb2pqr-dummy' in '/<<BUILDDIR>>/resolver-Q2SGA8/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-Q2SGA8/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ Sources [567 B]
Get:5 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ Packages [649 B]
Fetched 2549 B in 1s (3325 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 package was automatically installed and is no longer required:
netbase
Use 'apt autoremove' to remove it.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdmainutils debhelper
dh-autoreconf dh-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
libboost-iostreams1.67.0 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 libopenbabel6
libpipeline1 libpixman-1-0 libpng16-16 libpython3-dev libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev
libpython3.8-minimal libpython3.8-stdlib libschroedinger-maeparser1
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 pkg-config po-debconf python3 python3-dev python3-distutils
python3-lib2to3 python3-minimal python3-numpy python3-pkg-resources
python3.7 python3.7-minimal python3.8 python3.8-dev python3.8-minimal scons
sensible-utils sgml-base sgml-data swig swig4.0 ucf xml-core xmlto xsltproc
zlib1g-dev
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 python3-doc python3-tk
python3-venv python-numpy-doc python3-pytest python3-numpy-dbg
python3-setuptools python3.7-venv python3.7-doc binfmt-support
python3.8-venv python3.8-doc sgml-base-doc perlsgml w3-recs opensp swig-doc
swig-examples swig4.0-examples swig4.0-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
libboost-iostreams1.67.0 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 libopenbabel6
libpipeline1 libpixman-1-0 libpng16-16 libpython3-dev libpython3-stdlib
libpython3.7-minimal libpython3.7-stdlib libpython3.8 libpython3.8-dev
libpython3.8-minimal libpython3.8-stdlib libschroedinger-maeparser1
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 pkg-config po-debconf python3 python3-dev python3-distutils
python3-lib2to3 python3-minimal python3-numpy python3-pkg-resources
python3.7 python3.7-minimal python3.8 python3.8-dev python3.8-minimal
sbuild-build-depends-pdb2pqr-dummy scons sensible-utils sgml-base sgml-data
swig swig4.0 ucf xml-core xmlto xsltproc zlib1g-dev
0 upgraded, 104 newly installed, 0 to remove and 1 not upgraded.
Need to get 105 MB of archives.
After this operation, 308 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-Q2SGA8/apt_archive ./ sbuild-build-depends-pdb2pqr-dummy 0.invalid.0 [932 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf libtinfo5 armhf 6.2-1 [318 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf bsdmainutils armhf 11.1.2 [182 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-4 [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 2.9.1-1 [1262 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf libssl1.1 armhf 1.1.1d-2 [1268 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.2-1 [744 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.9-1 [71.5 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.2-1 [1628 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.8.2-2 [37.5 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 libmpdec2 armhf 2.4.2-3 [68.1 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.2-1 [1597 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.2-1 [410 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.8.2-2 [20.7 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.8.2-2 [62.6 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-minimal armhf 3.7.7-1 [585 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf python3.7-minimal armhf 3.7.7-1 [1532 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf sgml-base all 1.29.1 [15.0 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf sensible-utils all 0.0.12+nmu1 [16.0 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-4 [262 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-4 [112 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-4 [66.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0038+nmu1 [69.0 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.1-4 [771 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 12.10 [184 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.6.3-2 [14.7 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.176-1.1 [158 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.64.1-1 [1157 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libicu63 armhf 63.2-3 [7987 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-4 [592 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 12.10 [1003 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.2-2 [78.4 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.2-2 [145 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20200315 [91.6 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf sgml-data all 2.0.11 [179 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf docbook-xml all 4.5-9 [84.4 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf docbook-xsl all 1.79.1+dfsg-2 [1249 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf dos2unix armhf 7.4.0-2 [386 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-1 [1068 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-2 [280 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10-20200324-1+rpi1 [230 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-9-dev armhf 9.3.0-3+rpi1 [278 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf gfortran-9 armhf 9.3.0-3+rpi1 [8107 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:9.2.1-3.1+rpi1 [1440 B]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-1 [108 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf libboost-iostreams1.67.0 armhf 1.67.0-17 [246 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-2 [274 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.1-2 [330 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-2 [327 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.13.1-5 [133 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.9-2 [298 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.9-2 [692 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.13.1-5 [108 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.13.1-5 [99.4 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.9-1 [119 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-1 [1597 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libschroedinger-maeparser1 armhf 1.2.2-1 [72.5 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libopenbabel6 armhf 3.0.0+dfsg-3+b1 [3160 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8 armhf 3.8.2-1 [1367 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-dev armhf 3.8.2-1 [46.0 MB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libpython3-dev armhf 3.8.2-2 [20.9 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libpython3.7-stdlib armhf 3.7.7-1 [1670 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libxml2-utils armhf 2.9.10+dfsg-4 [104 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libxslt1.1 armhf 1.1.34-4 [218 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf openbabel armhf 3.0.0+dfsg-3+b1 [128 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29-6 [59.8 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf python3.8-dev armhf 3.8.2-1 [533 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf python3-dev armhf 3.8.2-2 [1168 B]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf python3.7 armhf 3.7.7-1 [354 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 44.0.0-1 [155 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf python3-numpy armhf 1:1.17.4-5+b1 [4484 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf scons all 3.1.2-2 [564 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf swig4.0 armhf 4.0.1-5 [1236 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf swig all 4.0.1-5 [329 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf xsltproc armhf 1.1.34-4 [123 kB]
Get:104 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 python3.7-minimal (3.7.7-1) ...
Setting up libgfortran5:armhf (10-20200324-1+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up sensible-utils (0.0.12+nmu1) ...
Setting up libuchardet0:armhf (0.0.6-3) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up sgml-base (1.29.1) ...
Setting up dos2unix (7.4.0-2) ...
Setting up libmpdec2:armhf (2.4.2-3) ...
Setting up swig4.0 (4.0.1-5) ...
Setting up libpython3.8-stdlib:armhf (3.8.2-1) ...
Setting up python3.8 (3.8.2-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up libtinfo5:armhf (6.2-1) ...
Setting up libelf1:armhf (0.176-1.1) ...
Setting up libxml2:armhf (2.9.10+dfsg-4) ...
Setting up libpython3-stdlib:armhf (3.8.2-2) ...
Setting up libfile-stripnondeterminism-perl (1.6.3-2) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libpython3.7-stdlib:armhf (3.7.7-1) ...
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 libxcb1:armhf (1.13.1-5) ...
Setting up swig (4.0.1-5) ...
Setting up libtool (2.4.6-14) ...
Setting up libxcb-render0:armhf (1.13.1-5) ...
Setting up libgfortran-9-dev:armhf (9.3.0-3+rpi1) ...
Setting up m4 (1.4.18-4) ...
Setting up python3 (3.8.2-2) ...
Setting up libxcb-shm0:armhf (1.13.1-5) ...
Setting up libschroedinger-maeparser1:armhf (1.2.2-1) ...
Setting up libfreetype6:armhf (2.10.1-2) ...
Setting up libpython3.8:armhf (3.8.2-1) ...
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 scons (3.1.2-2) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up ucf (3.0038+nmu1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.6.3-2) ...
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 (1.1.34-4) ...
Setting up libx11-6:armhf (2:1.6.9-2) ...
Setting up libxml2-utils (2.9.10+dfsg-4) ...
Setting up python3-lib2to3 (3.8.2-2) ...
Setting up python3-pkg-resources (44.0.0-1) ...
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-distutils (3.8.2-2) ...
Setting up dh-python (4.20200315) ...
Setting up python3.7 (3.7.7-1) ...
Setting up gettext (0.19.8.1-10) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up gfortran-9 (9.3.0-3+rpi1) ...
Setting up fontconfig-config (2.13.1-2) ...
Setting up xsltproc (1.1.34-4) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.1-1) ...
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 libpython3.8-dev:armhf (3.8.2-1) ...
Setting up python3-numpy (1:1.17.4-5+b1) ...
Setting up python3.8-dev (3.8.2-1) ...
Setting up libfontconfig1:armhf (2.13.1-2) ...
Setting up libpython3-dev:armhf (3.8.2-2) ...
Setting up po-debconf (1.0.21) ...
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up python3-dev (3.8.2-2) ...
Setting up libopenbabel6 (3.0.0+dfsg-3+b1) ...
Setting up openbabel (3.0.0+dfsg-3+b1) ...
Setting up debhelper (12.10) ...
Setting up dh-autoreconf (19) ...
Processing triggers for libc-bin (2.30-2+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_2.34-5+rpi1 dpkg-dev_1.19.7 g++-9_9.3.0-3+rpi1 gcc-9_9.3.0-3+rpi1 libc6-dev_2.30-2+rpi1 libstdc++-9-dev_9.3.0-3+rpi1 libstdc++6_10-20200324-1+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2
Package versions: adduser_3.118 apt_2.0.1 autoconf_2.69-11.1 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_5.0-6 binutils_2.34-5+rpi1 binutils-arm-linux-gnueabihf_2.34-5+rpi1 binutils-common_2.34-5+rpi1 bsdmainutils_11.1.2 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3 cpp_4:9.2.1-3.1+rpi1 cpp-9_9.3.0-3+rpi1 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.10 debianutils_4.9.1 dh-autoreconf_19 dh-python_4.20200315 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dirmngr_2.2.20-1 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_1.45.6-1 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 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_9.3.0-3+rpi1 gcc_4:9.2.1-3.1+rpi1 gcc-10-base_10-20200324-1+rpi1 gcc-6-base_6.5.0-1+rpi3 gcc-7-base_7.5.0-5 gcc-8-base_8.4.0-1+rpi1 gcc-9_9.3.0-3+rpi1 gcc-9-base_9.3.0-3+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:9.2.1-3.1+rpi1 gfortran-9_9.3.0-3+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.10-2 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 libacl1_2.2.53-6 libapt-pkg6.0_2.0.1 libarchive-zip-perl_1.68-1 libasan5_9.3.0-3+rpi1 libassuan0_2.5.3-7 libatomic1_10-20200324-1+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b2 libbinutils_2.34-5+rpi1 libblas3_3.9.0-1 libblkid1_2.34-0.1 libboost-iostreams1.67.0_1.67.0-17 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.30-2+rpi1 libc-dev-bin_2.30-2+rpi1 libc6_2.30-2+rpi1 libc6-dev_2.30-2+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200324-1+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.15-1 libcrypt1_1:4.4.15-1 libctf-nobfd0_2.34-5+rpi1 libctf0_2.34-5+rpi1 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.10 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libexpat1-dev_2.2.9-1 libext2fs2_1.45.6-1 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi7_3.3-3 libfile-stripnondeterminism-perl_1.6.3-2 libfontconfig1_2.13.1-2 libfreetype6_2.10.1-2 libgcc-9-dev_9.3.0-3+rpi1 libgcc-s1_10-20200324-1+rpi1 libgcc1_1:10-20200324-1+rpi1 libgcrypt20_1.8.5-5 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libgfortran-9-dev_9.3.0-3+rpi1 libgfortran5_10-20200324-1+rpi1 libglib2.0-0_2.64.1-1 libgmp10_2:6.2.0+dfsg-4 libgnutls30_3.6.12-2 libgomp1_10-20200324-1+rpi1 libgpg-error0_1.37-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-3 libidn2-0_2.3.0-1 libisl22_0.22.1-1 libksba8_1.3.5-2 liblapack3_3.9.0-1 libldap-2.4-2_2.4.49+dfsg-2 libldap-common_2.4.49+dfsg-2 liblocale-gettext-perl_1.07-4 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-3 libmpfr6_4.0.2-1 libncursesw6_6.2-1 libnettle7_3.5.1+really3.5.1-2 libnpth0_1.6-1 libopenbabel6_3.0.0+dfsg-3+b1 libp11-kit0_0.23.20-1 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_1.6.37-2 libpython3-dev_3.8.2-2 libpython3-stdlib_3.8.2-2 libpython3.7-minimal_3.7.7-1 libpython3.7-stdlib_3.7.7-1 libpython3.8_3.8.2-1 libpython3.8-dev_3.8.2-1 libpython3.8-minimal_3.8.2-1 libpython3.8-stdlib_3.8.2-1 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libschroedinger-maeparser1_1.2.2-1 libseccomp2_2.4.3-1+rpi1 libselinux1_3.0-1+b1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-4 libss2_1.45.6-1 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.3.0-3+rpi1 libstdc++6_10-20200324-1+rpi1 libsub-override-perl_0.09-2 libsystemd0_244.3-1+rpi1 libtasn1-6_4.16.0-2 libtext-charwidth-perl_0.04-10 libtext-iconv-perl_1.7-7 libtinfo5_6.2-1 libtinfo6_6.2-1 libtool_2.4.6-14 libubsan1_10-20200324-1+rpi1 libuchardet0_0.0.6-3 libudev1_244.3-1+rpi1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libx11-6_2:1.6.9-2 libx11-data_2:1.6.9-2 libxau6_1:1.0.8-1+b2 libxcb-render0_1.13.1-5 libxcb-shm0_1.13.1-5 libxcb1_1.13.1-5 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-4 libxml2-utils_2.9.10+dfsg-4 libxrender1_1:0.9.10-1 libxslt1.1_1.1.34-4 libzstd1_1.4.4+dfsg-3+rpi1 linux-libc-dev_5.2.17-1+rpi1+b2 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.1-1 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.2-1 ncurses-bin_6.2-1 netbase_6.1 openbabel_3.0.0+dfsg-3+b1 passwd_1:4.8.1-1 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 pkg-config_0.29-6 po-debconf_1.0.21 python3_3.8.2-2 python3-dev_3.8.2-2 python3-distutils_3.8.2-2 python3-lib2to3_3.8.2-2 python3-minimal_3.8.2-2 python3-numpy_1:1.17.4-5+b1 python3-pkg-resources_44.0.0-1 python3.7_3.7.7-1 python3.7-minimal_3.7.7-1 python3.8_3.8.2-1 python3.8-dev_3.8.2-1 python3.8-minimal_3.8.2-1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pdb2pqr-dummy_0.invalid.0 scons_3.1.2-2 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.29.1 sgml-data_2.0.11 swig_4.0.1-5 swig4.0_4.0.1-5 sysvinit-utils_2.96-3 tar_1.30+dfsg-7 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_1.1.34-4 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error
gpgv: Signature made Thu Mar 26 19:17:18 2020 UTC
gpgv: using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pdb2pqr_2.1.1+dfsg-6.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-6.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
dpkg-source: info: applying python3_PR516.patch
dpkg-source: info: applying python3_scons.patch
dpkg-source: info: applying python3_sundry.patch
dpkg-source: info: applying python3_scriptbang.patch
dpkg-source: info: applying use_pkg-config.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=root
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-b2d8f63a-531c-4e09-9f29-cfecc97c2eb0
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=xterm
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pdb2pqr
dpkg-buildpackage: info: source version 2.1.1+dfsg-6
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
fakeroot debian/rules clean
dh clean --with python3
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 python3
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 )
scons \
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/python3.8 -I/usr/include/arm-linux-gnueabihf/python3.8 -I/usr/include/python3.8 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/substruct/Algorithms.cpp
In file included from /usr/include/python3.8/numpy/ndarraytypes.h:1830,
from /usr/include/python3.8/numpy/ndarrayobject.h:12,
from /usr/include/python3.8/numpy/arrayobject.h:4,
from pdb2pka/substruct/Algorithms.cpp:43:
/usr/include/python3.8/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 " \
| ^~~~~~~
pdb2pka/substruct/Algorithms.cpp: In function 'PyObject* initAlgorithms()':
pdb2pka/substruct/Algorithms.cpp:333:1: warning: control reaches end of non-void function [-Wreturn-type]
333 | };
| ^
g++ -o pdb2pka/substruct/Algorithms.cpython-38-arm-linux-gnueabihf.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib
g++ -o pdb2pka/pMC_mult.os -c -g -fPIC -I/usr/include/python3.8 -I/usr/include/arm-linux-gnueabihf/python3.8 -I/usr/include/python3.8 -I/usr/lib/python3/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/python3.8 -I/usr/include/arm-linux-gnueabihf/python3.8 -I/usr/include/python3.8 -I/usr/lib/python3/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:4807:44: 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
4807 | 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:4807:171: 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
4807 | 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:4808:44: 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
4808 | 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:4808:44: 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:4808:218: 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
4808 | 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:4809:44: 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
4809 | 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:4809:219: 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
4809 | 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:4810:17: 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
4810 | 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:4810:223: 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
4810 | 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*, Py_ssize_t, PyObject**)':
pdb2pka/pMC_mult_wrap.cpp:8807:60: 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
8807 | 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*, Py_ssize_t, PyObject**)':
pdb2pka/pMC_mult_wrap.cpp:8857:65: 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
8857 | 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*, Py_ssize_t, PyObject**)':
pdb2pka/pMC_mult_wrap.cpp:9248:83: 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
9248 | 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*, Py_ssize_t, PyObject**)':
pdb2pka/pMC_mult_wrap.cpp:9301:42: 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
9301 | 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:2783:
/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:4122:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4122 | return new SwigPyIteratorClosed_T<OutIter>(current, begin, end, seq);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4122:12: 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:3741:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
3741 | 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:3787:33: 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
3787 | self->insert(std::copy(is.begin(), isit, sb), isit, is.end());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:3787:11: 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
3787 | self->insert(std::copy(is.begin(), isit, sb), isit, is.end());
| ^~~~
pdb2pka/pMC_mult_wrap.cpp:3787:11: 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:3794:11: 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
3794 | self->erase(sb,se);
| ^~~~
pdb2pka/pMC_mult_wrap.cpp:3797:11: 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
3797 | self->insert(sb, is.begin(), is.end());
| ^~~~
pdb2pka/pMC_mult_wrap.cpp:3797:11: 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:3846:9: 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
3846 | self->erase(sb,se);
| ^~~~
pdb2pka/pMC_mult_wrap.cpp:3851:14: 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
3851 | it = self->erase(it);
pdb2pka/pMC_mult_wrap.cpp:3863:9: 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
3863 | it = typename Sequence::reverse_iterator(self->erase((++it).base()));
| ^~
pdb2pka/pMC_mult_wrap.cpp:3863:9: 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:3717:5: 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
3717 | 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:2783:
/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:2783:
/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:2783:
/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:4136:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4136 | 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:2783:
/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:2783:
/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:2783:
/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:4092:5: 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
4092 | SwigPyIteratorClosed_T(out_iterator curr, out_iterator first, out_iterator last, PyObject *seq)
| ^~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4092:5: 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:4092:5: 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:4093:93: 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
4093 | : SwigPyForwardIteratorClosed_T<OutIterator,ValueType,FromOper>(curr, first, last, seq)
| ^
pdb2pka/pMC_mult_wrap.cpp:4093:93: 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
In file included from /usr/include/c++/9/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2783:
/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:2710:
/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:2783:
/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:2710:
/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:2783:
/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:2710:
/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:2783:
/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:2710:
/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:2783:
/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:4018:5: 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
4018 | SwigPyIteratorOpen_T(out_iterator curr, PyObject *seq)
| ^~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4019:59: 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
4019 | : SwigPyForwardIteratorOpen_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:2783:
/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:2783:
/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:2783:
/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:2783:
/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::SwigPyForwardIteratorClosed_T<OutIterator, ValueType, FromOper>::SwigPyForwardIteratorClosed_T(swig::SwigPyForwardIteratorClosed_T<OutIterator, ValueType, FromOper>::out_iterator, swig::SwigPyForwardIteratorClosed_T<OutIterator, ValueType, FromOper>::out_iterator, swig::SwigPyForwardIteratorClosed_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:4044:5: note: parameter passing for argument of type 'swig::SwigPyForwardIteratorClosed_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
4044 | SwigPyForwardIteratorClosed_T(out_iterator curr, out_iterator first, out_iterator last, PyObject *seq)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4044:5: note: parameter passing for argument of type 'swig::SwigPyForwardIteratorClosed_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:4044:5: note: parameter passing for argument of type 'swig::SwigPyForwardIteratorClosed_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:4045:73: note: parameter passing for argument of type 'swig::SwigPyForwardIteratorClosed_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
4045 | : 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:2783:
/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:2710:
/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/python3.8/pyport.h:212,
from /usr/include/python3.8/Python.h:63,
from pdb2pka/pMC_mult_wrap.cpp:178:
/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:2710:
/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:2783:
/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:2783:
/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:2710:
/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:2783:
/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);
| ~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp: In constructor 'swig::SwigPyForwardIteratorOpen_T<OutIterator, ValueType, FromOper>::SwigPyForwardIteratorOpen_T(swig::SwigPyForwardIteratorOpen_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:3982:5: note: parameter passing for argument of type 'swig::SwigPyForwardIteratorOpen_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
3982 | SwigPyForwardIteratorOpen_T(out_iterator curr, PyObject *seq)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:3983:48: note: parameter passing for argument of type 'swig::SwigPyForwardIteratorOpen_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
3983 | : SwigPyIterator_T<OutIterator>(curr, seq)
| ^
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:2710:
/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:2783:
/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:2783:
/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:2783:
/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); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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:3924:5: 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
3924 | SwigPyIterator_T(out_iterator curr, PyObject *seq)
| ^~~~~~~~~~~~~~~~
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:2710:
/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:2710:
/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:2710:
/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:2783:
/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/python3.8/pyport.h:212,
from /usr/include/python3.8/Python.h:63,
from pdb2pka/pMC_mult_wrap.cpp:178:
/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:2710:
/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:4421:7: 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
4421 | 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:2783:
/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:2783:
/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:2710:
/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:2710:
/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:2783:
/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:2783:
/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:2710:
/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:2783:
/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:2710:
/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:2783:
/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:2710:
/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:3949:22: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
3949 | 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:2710:
/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.cpython-38-arm-linux-gnueabihf.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/pMC_mult.os pdb2pka/pMC_mult_wrap.os -L/usr/lib
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.cpython-38-arm-linux-gnueabihf.so', 'pdb2pka/_pMC_mult.cpython-38-arm-linux-gnueabihf.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 python3 that you intend to use with pdb2pqr.
For example: "scons" will setup pdb2pqr to be run with Debian default Python3 interpreter
Run "scons install" to install pdb2pqr in /usr/share/pdb2pqr/
Run "scons basic-test" for a basic functionality test
Run "scons advanced-test" for a single test of ligand and PROPKA support. Requires numpy and PDB2PKA support compiled.
Run "scons complete-test" for a complete test of all functionality EXCEPT PDB2PKA. Requires numpy and PDB2PKA support compiled.
Run "scons pdb2pka-test" for a test of PDB2PKA functionality.
Requires numpy, PDB2PKA support compiled AND the APBS python3 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 install"
Run "scons 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 python3
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'
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installexamples
for bakerdoc in $( grep -l "http://agave.wustl.edu/css/baker.css" -R debian/pdb2pqr-doc/usr/share/doc/pdb2pqr/* ); do \
sed "s|href=\"http://agave.wustl.edu/css/baker.css\"|href=\"baker.css\"|g" -i $bakerdoc; done
grep: debian/pdb2pqr-doc/usr/share/doc/pdb2pqr/*: No such file or directory
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
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_python3 -a
dh_perl -a
debian/rules override_dh_link-arch
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_link -a
dh_link -a usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-38-arm-linux-gnueabihf.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
dh_link -a usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-38-arm-linux-gnueabihf.so usr/share/pdb2pqr/pdb2pka/substruct/Algorithms.so
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
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_dwz -a
dh_strip -a
dh_makeshlibs -a
dh_shlibdeps -a
dh_installdeb -a
dh_gencontrol -a
dh_md5sums -a
dh_builddeb -a
dpkg-deb: building package 'pdb2pqr-dbgsym' in '../pdb2pqr-dbgsym_2.1.1+dfsg-6_armhf.deb'.
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-6_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pdb2pqr_2.1.1+dfsg-6_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 2020-03-30T21:45:08Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pdb2pqr_2.1.1+dfsg-6_armhf.changes:
-----------------------------------
Format: 1.8
Date: Fri, 27 Mar 2020 03:08:11 +0800
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-dbgsym
Architecture: armhf
Version: 2.1.1+dfsg-6
Distribution: bullseye-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Drew Parsons <dparsons@debian.org>
Description:
pdb2pqr - Preparation of protein structures for electrostatics calculations
Closes: 937262
Changes:
pdb2pqr (2.1.1+dfsg-6) unstable; urgency=medium
.
* Team upload.
.
[ Andreas Tille ]
* python3_scons.patch, python3_sundry.patch port Scons and other
sundry files from Python2 to Python3 missed by upstream PR#516.
Closes: #937262.
* Re-activate other part of autopkgtest
* debhelper-compat 12
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/control
* Remove trailing whitespace in debian/copyright
* Remove obsolete field Name from debian/upstream/metadata.
* Use Debian packaged scons
TODO: convince scons to install do $(CURDIR)/debian/tmp
.
[ Drew Parsons ]
* Use python3_PR516.patch to apply upstream PR#516 porting from
Python2 to Python3.
* python3_scriptbang.patch updates script hashbangs to python3
* Standards-Version: 4.5.0
* close privacy breach by replacing hrefs to
http://agave.wustl.edu/css/baker.css (which is no longer
available) to baker.css
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Files:
cbc966f3c4b72d5e3c3b97b599269ffd 301128 debug optional pdb2pqr-dbgsym_2.1.1+dfsg-6_armhf.deb
fd844e39d996a0ab00a01afaa0c16852 6726 science optional pdb2pqr_2.1.1+dfsg-6_armhf.buildinfo
151693dd0075e3e210ef0b013c335d43 370068 science optional pdb2pqr_2.1.1+dfsg-6_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pdb2pqr-dbgsym_2.1.1+dfsg-6_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 301128 bytes: control archive=648 bytes.
421 bytes, 12 lines control
299 bytes, 3 lines md5sums
Package: pdb2pqr-dbgsym
Source: pdb2pqr
Version: 2.1.1+dfsg-6
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 530
Depends: pdb2pqr (= 2.1.1+dfsg-6)
Section: debug
Priority: optional
Description: debug symbols for pdb2pqr
Build-Ids: 445a9247ad05e0e56d58d2836c3bb5e627cceeca 4c87e80ab321c1c3caebe309cd3d43aa0a3158bb
drwxr-xr-x root/root 0 2020-03-26 19:08 ./
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/debug/.build-id/44/
-rw-r--r-- root/root 16540 2020-03-26 19:08 ./usr/lib/debug/.build-id/44/5a9247ad05e0e56d58d2836c3bb5e627cceeca.debug
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/debug/.build-id/4c/
-rw-r--r-- root/root 491828 2020-03-26 19:08 ./usr/lib/debug/.build-id/4c/87e80ab321c1c3caebe309cd3d43aa0a3158bb.debug
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 19076 2020-03-26 19:08 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/pdb2pqr.debug
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-03-26 19:08 ./usr/share/doc/pdb2pqr-dbgsym -> pdb2pqr
pdb2pqr_2.1.1+dfsg-6_armhf.deb
------------------------------
new Debian package, version 2.0.
size 370068 bytes: control archive=4804 bytes.
1409 bytes, 28 lines control
9687 bytes, 130 lines md5sums
275 bytes, 12 lines * postinst #!/bin/sh
388 bytes, 12 lines * prerm #!/bin/sh
Package: pdb2pqr
Version: 2.1.1+dfsg-6
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2841
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2), python3 (<< 3.9), python3 (>= 3.8~), python3:any, python3-numpy, python3-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 2020-03-26 19:08 ./
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/bin/
lrwxrwxrwx root/root 0 2020-03-26 19:08 ./usr/bin/pdb2pqr -> ../share/pdb2pqr/pdb2pqr.py
lrwxrwxrwx root/root 0 2020-03-26 19:08 ./usr/bin/propka -> ../share/pdb2pqr/propka30/propka.py
lrwxrwxrwx root/root 0 2020-03-26 19:08 ./usr/bin/psize -> ../share/pdb2pqr/src/psize.py
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/pdb2pqr/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/pdb2pqr/pdb2pka/
-rw-r--r-- root/root 578516 2020-03-26 19:08 ./usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-38-arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/lib/pdb2pqr/pdb2pka/substruct/
-rw-r--r-- root/root 14620 2020-03-26 19:08 ./usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-38-arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/doc/pdb2pqr/
-rw-r--r-- root/root 31 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/AUTHORS
-rw-r--r-- root/root 175 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/NEWS.gz
-rw-r--r-- root/root 783 2020-03-26 19:08 ./usr/share/doc/pdb2pqr/README.Debian
-rw-r--r-- root/root 688 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/README.md
-rw-r--r-- root/root 2516 2020-03-26 19:08 ./usr/share/doc/pdb2pqr/changelog.Debian.gz
-rw-r--r-- root/root 613 2016-03-08 20:40 ./usr/share/doc/pdb2pqr/changelog.gz
-rw-r--r-- root/root 5186 2020-03-26 19:08 ./usr/share/doc/pdb2pqr/copyright
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/man/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/man/man1/
-rw-r--r-- root/root 2082 2020-03-26 19:08 ./usr/share/man/man1/pdb2pqr.1.gz
-rw-r--r-- root/root 1044 2020-03-26 19:08 ./usr/share/man/man1/propka.1.gz
-rw-r--r-- root/root 1252 2020-03-26 19:08 ./usr/share/man/man1/psize.1.gz
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/pdb2pqr/
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/pdb2pqr/dat/
-rw-r--r-- root/root 61111 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/AA.xml
-rw-r--r-- root/root 62938 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/AMBER.DAT
-rw-r--r-- root/root 2398 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/AMBER.names
-rw-r--r-- root/root 66828 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/CHARMM.DAT
-rw-r--r-- root/root 7123 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/CHARMM.names
-rw-r--r-- root/root 4633 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/HYDROGENS.xml
-rw-r--r-- root/root 35389 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/NA.xml
-rw-r--r-- root/root 25519 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/PARSE.DAT
-rw-r--r-- root/root 5921 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/PARSE.names
-rw-r--r-- root/root 15461 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/PATCHES.xml
-rw-r--r-- root/root 30813 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/PEOEPB.DAT
-rw-r--r-- root/root 1738 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/PEOEPB.names
-rw-r--r-- root/root 35461 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/SWANSON.DAT
-rw-r--r-- root/root 1245 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/SWANSON.names
-rw-r--r-- root/root 65298 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/TOPOLOGY.xml
-rw-r--r-- root/root 99831 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/TYL06.DAT
-rw-r--r-- root/root 2087 2016-02-18 19:56 ./usr/share/pdb2pqr/dat/TYL06.names
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/pdb2pqr/extensions/
-rw-r--r-- root/root 209 2016-02-18 19:56 ./usr/share/pdb2pqr/extensions/README
-rw-r--r-- root/root 4747 2020-03-26 19:08 ./usr/share/pdb2pqr/extensions/__init__.py
-rw-r--r-- root/root 2011 2016-02-18 19:56 ./usr/share/pdb2pqr/extensions/chi.py
-rw-r--r-- root/root 2923 2016-02-18 19:56 ./usr/share/pdb2pqr/extensions/contact.py
-rw-r--r-- root/root 7147 2016-02-18 19:56 ./usr/share/pdb2pqr/extensions/hbond.py
-rw-r--r-- root/root 13553 2020-03-26 19:08 ./usr/share/pdb2pqr/extensions/newresinter.py
-rw-r--r-- root/root 3441 2016-02-18 19:56 ./usr/share/pdb2pqr/extensions/rama.py
-rw-r--r-- root/root 12513 2020-03-26 19:08 ./usr/share/pdb2pqr/extensions/resinter.py
-rw-r--r-- root/root 3139 2020-03-26 19:08 ./usr/share/pdb2pqr/extensions/salt.py
-rw-r--r-- root/root 944 2016-02-18 19:56 ./usr/share/pdb2pqr/extensions/summary.py
-rw-r--r-- root/root 3303 2016-02-18 19:56 ./usr/share/pdb2pqr/extensions/template
-rw-r--r-- root/root 34647 2020-03-26 19:08 ./usr/share/pdb2pqr/main.py
-rw-r--r-- root/root 28310 2020-03-26 19:08 ./usr/share/pdb2pqr/main_cgi.py
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/
-rw-r--r-- root/root 29181 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/NEWligand_topology.py
-rw-r--r-- root/root 0 2016-02-18 19:56 ./usr/share/pdb2pqr/pdb2pka/__init__.py
lrwxrwxrwx root/root 0 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/_pMC_mult.so -> ../../../lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-38-arm-linux-gnueabihf.so
-rw-r--r-- root/root 15131 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/apbs.py
-rw-r--r-- root/root 3539 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/charge_mon.py
-rw-r--r-- root/root 8208 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/example.py
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/graph_cut/
-rw-r--r-- root/root 0 2016-02-18 19:56 ./usr/share/pdb2pqr/pdb2pka/graph_cut/__init__.py
-rw-r--r-- root/root 375 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/graph_cut/create_titration_output.py
-rw-r--r-- root/root 4365 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/graph_cut/graph.py
-rw-r--r-- root/root 36927 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/graph_cut/protein_complex.py
-rw-r--r-- root/root 8380 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/graph_cut/titration_curve.py
-rw-r--r-- root/root 4060 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/graph_cut/uncertainty.py
-rw-r--r-- root/root 4046 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/graph_cut/utils.py
-rw-r--r-- root/root 11732 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/inputgen_pKa.py
-rw-r--r-- root/root 29224 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/ligand_topology.py
drwxr-xr-x root/root 0 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/ligandclean/
-rw-r--r-- root/root 28 2016-02-18 19:56 ./usr/share/pdb2pqr/pdb2pka/ligandclean/__init__.py
-rw-r--r-- root/root 14018 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/ligandclean/ligff.py
-rw-r--r-- root/root 1013 2016-02-18 19:56 ./usr/share/pdb2pqr/pdb2pka/ligandclean/lookuptable.py
-rw-r--r-- root/root 5526 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/ligandclean/peoe_PDB2PQR.py
-rw-r--r-- root/root 4074 2016-02-18 19:56 ./usr/share/pdb2pqr/pdb2pka/ligandclean/templates.py
-rw-r--r-- root/root 4749 2016-02-18 19:56 ./usr/share/pdb2pqr/pdb2pka/ligandclean/trial_templates.py
-rw-r--r-- root/root 34865 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/pKaIO_compat.py
-rw-r--r-- root/root 5050 2016-02-18 19:56 ./usr/share/pdb2pqr/pdb2pka/pKa_base.py
-rw-r--r-- root/root 5712 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/pKa_utility_functions_compat.py
-rw-r--r-- root/root 13335 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/pMC_mult.py
-rw-r--r-- root/root 3878 2020-03-26 19:08 ./usr/share/pdb2pqr/pdb2pka/pka_help.py
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| Post Build |
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| Cleanup |
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Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
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| Summary |
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Build Architecture: armhf
Build-Space: 56824
Build-Time: 116
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 602
Job: pdb2pqr_2.1.1+dfsg-6
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 776
Source-Version: 2.1.1+dfsg-6
Space: 56824
Status: successful
Version: 2.1.1+dfsg-6
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Finished at 2020-03-30T21:45:08Z
Build needed 00:12:56, 56824k disc space