pdb2pqr →
2.1.1+dfsg-8 →
armhf → 2022-02-13 13:16:34
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-02
+==============================================================================+
| pdb2pqr 2.1.1+dfsg-8 (armhf) Sun, 13 Feb 2022 12:56:24 +0000 |
+==============================================================================+
Package: pdb2pqr
Version: 2.1.1+dfsg-8
Source Version: 2.1.1+dfsg-8
Distribution: bookworm-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bookworm-staging-armhf-sbuild-1b47db7a-f477-4290-a7ca-276501f16c21' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.4.1/private bookworm-staging InRelease [11.3 kB]
Get:2 http://172.17.4.1/private bookworm-staging/main Sources [12.8 MB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf Packages [13.6 MB]
Fetched 26.4 MB in 28s (956 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://172.17.4.1/private bookworm-staging/main pdb2pqr 2.1.1+dfsg-8 (dsc) [2267 B]
Get:2 http://172.17.4.1/private bookworm-staging/main pdb2pqr 2.1.1+dfsg-8 (tar) [5191 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main pdb2pqr 2.1.1+dfsg-8 (diff) [67.6 kB]
Fetched 5261 kB in 1s (9776 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pdb2pqr-38MIDR/pdb2pqr-2.1.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-38MIDR' 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-U4frHv/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-U4frHv/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-U4frHv/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-U4frHv/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ Packages [432 B]
Fetched 2108 B in 1s (2778 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libperl5.32 netbase perl-modules-5.32 sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 19 not upgraded.
Need to get 848 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [848 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 848 B in 0s (22.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 14442 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-U4frHv/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-U4frHv/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ Sources [567 B]
Get:5 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ Packages [648 B]
Fetched 2548 B in 1s (3078 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install pdb2pqr build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libperl5.32 netbase perl-modules-5.32
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils cpp-11 debhelper
dh-autoreconf dh-python dh-strip-nondeterminism docbook-xml docbook-xsl
dos2unix dwz file fontconfig-config fonts-dejavu-core g++-11 gcc-11
gcc-11-base gettext gettext-base gfortran gfortran-11 groff-base
intltool-debian libarchive-zip-perl libasan6 libatomic1 libblas3
libboost-iostreams1.71.0 libbrotli1 libbsd0 libcairo2 libcc1-0
libdebhelper-perl libelf1 libexpat1 libexpat1-dev
libfile-stripnondeterminism-perl libfontconfig1 libfreetype6 libgcc-11-dev
libgcc-s1 libgfortran-11-dev libgfortran5 libglib2.0-0 libgomp1 libicu67
libinchi1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
libmaeparser1 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenbabel7
libpipeline1 libpixman-1-0 libpng16-16 libpython3-dev libpython3-stdlib
libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libstdc++-11-dev libstdc++6 libsub-override-perl libtool
libubsan1 libuchardet0 libx11-6 libx11-data libxau6 libxcb-render0
libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2 libxml2-utils libxrender1
libxslt1.1 m4 man-db media-types openbabel pkg-config po-debconf python3
python3-dev python3-distutils python3-lib2to3 python3-minimal python3-numpy
python3-pkg-resources python3.9 python3.9-dev python3.9-minimal scons
sgml-base sgml-data swig swig4.0 ucf xml-core xmlto xsltproc zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc gcc-11-locales dh-make flit
python3-build python3-tomli python3-installer 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 gcc-11-doc gettext-doc libasprintf-dev
libgettextpo-dev gfortran-doc gfortran-11-doc libcoarrays-dev groff
libstdc++-11-doc 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-setuptools python3.9-venv python3.9-doc
binfmt-support 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 javascript-common ca-certificates libltdl-dev
libmail-sendmail-perl dblatex | fop libpaper-utils zip
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev bsdextrautils 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-11 groff-base intltool-debian libarchive-zip-perl libblas3
libboost-iostreams1.71.0 libbrotli1 libbsd0 libcairo2 libdebhelper-perl
libelf1 libexpat1 libexpat1-dev libfile-stripnondeterminism-perl
libfontconfig1 libfreetype6 libgfortran-11-dev libgfortran5 libglib2.0-0
libicu67 libinchi1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3
libmaeparser1 libmagic-mgc libmagic1 libmd0 libmpdec3 libopenbabel7
libpipeline1 libpixman-1-0 libpng16-16 libpython3-dev libpython3-stdlib
libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libsub-override-perl libtool libuchardet0 libx11-6 libx11-data
libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxml2
libxml2-utils libxrender1 libxslt1.1 m4 man-db media-types openbabel
pkg-config po-debconf python3 python3-dev python3-distutils python3-lib2to3
python3-minimal python3-numpy python3-pkg-resources python3.9 python3.9-dev
python3.9-minimal sbuild-build-depends-pdb2pqr-dummy scons sgml-base
sgml-data swig swig4.0 ucf xml-core xmlto xsltproc zlib1g-dev
The following packages will be upgraded:
cpp-11 g++-11 gcc-11 gcc-11-base libasan6 libatomic1 libcc1-0 libgcc-11-dev
libgcc-s1 libgomp1 libstdc++-11-dev libstdc++6 libubsan1
13 upgraded, 102 newly installed, 0 to remove and 6 not upgraded.
Need to get 91.9 MB of archives.
After this operation, 224 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-U4frHv/apt_archive ./ sbuild-build-depends-pdb2pqr-dummy 0.invalid.0 [932 B]
Get:2 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-minimal armhf 3.9.10-1+rpi1 [794 kB]
Get:3 http://172.17.4.1/private bookworm-staging/main armhf libcc1-0 armhf 11.2.0-16+rpi1 [37.7 kB]
Get:4 http://172.17.4.1/private bookworm-staging/main armhf gcc-11-base armhf 11.2.0-16+rpi1 [207 kB]
Get:5 http://172.17.4.1/private bookworm-staging/main armhf libgcc-s1 armhf 11.2.0-16+rpi1 [36.2 kB]
Get:6 http://172.17.4.1/private bookworm-staging/main armhf libgomp1 armhf 11.2.0-16+rpi1 [87.9 kB]
Get:7 http://172.17.4.1/private bookworm-staging/main armhf libatomic1 armhf 11.2.0-16+rpi1 [8180 B]
Get:8 http://172.17.4.1/private bookworm-staging/main armhf libasan6 armhf 11.2.0-16+rpi1 [1946 kB]
Get:9 http://172.17.4.1/private bookworm-staging/main armhf libubsan1 armhf 11.2.0-16+rpi1 [798 kB]
Get:10 http://172.17.4.1/private bookworm-staging/main armhf g++-11 armhf 11.2.0-16+rpi1 [7914 kB]
Get:11 http://172.17.4.1/private bookworm-staging/main armhf libstdc++-11-dev armhf 11.2.0-16+rpi1 [1963 kB]
Get:12 http://172.17.4.1/private bookworm-staging/main armhf libgcc-11-dev armhf 11.2.0-16+rpi1 [696 kB]
Get:13 http://172.17.4.1/private bookworm-staging/main armhf gcc-11 armhf 11.2.0-16+rpi1 [14.0 MB]
Get:14 http://172.17.4.1/private bookworm-staging/main armhf cpp-11 armhf 11.2.0-16+rpi1 [7074 kB]
Get:15 http://172.17.4.1/private bookworm-staging/main armhf libstdc++6 armhf 11.2.0-16+rpi1 [466 kB]
Get:16 http://172.17.4.1/private bookworm-staging/main armhf libexpat1 armhf 2.4.4-1 [82.4 kB]
Get:17 http://172.17.4.1/private bookworm-staging/main armhf python3.9-minimal armhf 3.9.10-1+rpi1 [1595 kB]
Get:18 http://172.17.4.1/private bookworm-staging/main armhf python3-minimal armhf 3.9.7-1+b4 [38.7 kB]
Get:19 http://172.17.4.1/private bookworm-staging/main armhf media-types all 5.0.0 [32.5 kB]
Get:20 http://172.17.4.1/private bookworm-staging/main armhf libmpdec3 armhf 2.5.1-2+rpi1 [73.5 kB]
Get:21 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-stdlib armhf 3.9.10-1+rpi1 [1611 kB]
Get:22 http://172.17.4.1/private bookworm-staging/main armhf python3.9 armhf 3.9.10-1+rpi1 [488 kB]
Get:23 http://172.17.4.1/private bookworm-staging/main armhf libpython3-stdlib armhf 3.9.7-1+b4 [21.8 kB]
Get:24 http://172.17.4.1/private bookworm-staging/main armhf python3 armhf 3.9.7-1+b4 [38.3 kB]
Get:25 http://172.17.4.1/private bookworm-staging/main armhf sgml-base all 1.30 [15.1 kB]
Get:26 http://172.17.4.1/private bookworm-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:27 http://172.17.4.1/private bookworm-staging/main armhf groff-base armhf 1.22.4-8 [793 kB]
Get:28 http://172.17.4.1/private bookworm-staging/main armhf bsdextrautils armhf 2.37.3-1 [136 kB]
Get:29 http://172.17.4.1/private bookworm-staging/main armhf libpipeline1 armhf 1.5.5-1 [32.9 kB]
Get:30 http://172.17.4.1/private bookworm-staging/main armhf man-db armhf 2.10.0-2 [1356 kB]
Get:31 http://172.17.4.1/private bookworm-staging/main armhf libmagic-mgc armhf 1:5.41-2 [295 kB]
Get:32 http://172.17.4.1/private bookworm-staging/main armhf libmagic1 armhf 1:5.41-2 [119 kB]
Get:33 http://172.17.4.1/private bookworm-staging/main armhf file armhf 1:5.41-2 [65.8 kB]
Get:34 http://172.17.4.1/private bookworm-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:35 http://172.17.4.1/private bookworm-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:36 http://172.17.4.1/private bookworm-staging/main armhf libsigsegv2 armhf 2.14-1 [36.6 kB]
Get:37 http://172.17.4.1/private bookworm-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:38 http://172.17.4.1/private bookworm-staging/main armhf autoconf all 2.71-2 [343 kB]
Get:39 http://172.17.4.1/private bookworm-staging/main armhf autotools-dev all 20220109.1 [51.6 kB]
Get:40 http://172.17.4.1/private bookworm-staging/main armhf automake all 1:1.16.5-1.1 [823 kB]
Get:41 http://172.17.4.1/private bookworm-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:42 http://172.17.4.1/private bookworm-staging/main armhf libdebhelper-perl all 13.6 [193 kB]
Get:43 http://172.17.4.1/private bookworm-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:44 http://172.17.4.1/private bookworm-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:45 http://172.17.4.1/private bookworm-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:46 http://172.17.4.1/private bookworm-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:47 http://172.17.4.1/private bookworm-staging/main armhf libfile-stripnondeterminism-perl all 1.13.0-1 [26.6 kB]
Get:48 http://172.17.4.1/private bookworm-staging/main armhf dh-strip-nondeterminism all 1.13.0-1 [15.8 kB]
Get:49 http://172.17.4.1/private bookworm-staging/main armhf libelf1 armhf 0.186-1 [174 kB]
Get:50 http://172.17.4.1/private bookworm-staging/main armhf dwz armhf 0.14-1 [83.0 kB]
Get:51 http://172.17.4.1/private bookworm-staging/main armhf libicu67 armhf 67.1-7 [8291 kB]
Get:52 http://172.17.4.1/private bookworm-staging/main armhf libxml2 armhf 2.9.12+dfsg-5 [584 kB]
Get:53 http://172.17.4.1/private bookworm-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:54 http://172.17.4.1/private bookworm-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:55 http://172.17.4.1/private bookworm-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:56 http://172.17.4.1/private bookworm-staging/main armhf debhelper all 13.6 [1054 kB]
Get:57 http://172.17.4.1/private bookworm-staging/main armhf python3-lib2to3 all 3.9.10-1 [79.4 kB]
Get:58 http://172.17.4.1/private bookworm-staging/main armhf python3-distutils all 3.9.10-1 [146 kB]
Get:59 http://172.17.4.1/private bookworm-staging/main armhf dh-python all 5.20220119 [110 kB]
Get:60 http://172.17.4.1/private bookworm-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:61 http://172.17.4.1/private bookworm-staging/main armhf sgml-data all 2.0.11+nmu1 [179 kB]
Get:62 http://172.17.4.1/private bookworm-staging/main armhf docbook-xml all 4.5-11 [85.0 kB]
Get:63 http://172.17.4.1/private bookworm-staging/main armhf docbook-xsl all 1.79.2+dfsg-1 [1237 kB]
Get:64 http://172.17.4.1/private bookworm-staging/main armhf dos2unix armhf 7.4.2-2 [391 kB]
Get:65 http://172.17.4.1/private bookworm-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:66 http://172.17.4.1/private bookworm-staging/main armhf fontconfig-config all 2.13.1-4.4 [281 kB]
Get:67 http://172.17.4.1/private bookworm-staging/main armhf libgfortran5 armhf 11.2.0-16+rpi1 [235 kB]
Get:68 http://172.17.4.1/private bookworm-staging/main armhf libgfortran-11-dev armhf 11.2.0-16+rpi1 [280 kB]
Get:69 http://172.17.4.1/private bookworm-staging/main armhf gfortran-11 armhf 11.2.0-16+rpi1 [7578 kB]
Get:70 http://172.17.4.1/private bookworm-staging/main armhf gfortran armhf 4:11.2.0-2+rpi1 [1428 B]
Get:71 http://172.17.4.1/private bookworm-staging/main armhf libblas3 armhf 3.10.0-2 [109 kB]
Get:72 http://172.17.4.1/private bookworm-staging/main armhf libboost-iostreams1.71.0 armhf 1.71.0-7+b1 [256 kB]
Get:73 http://172.17.4.1/private bookworm-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:74 http://172.17.4.1/private bookworm-staging/main armhf libmd0 armhf 1.0.4-1 [28.9 kB]
Get:75 http://172.17.4.1/private bookworm-staging/main armhf libbsd0 armhf 0.11.5-1 [108 kB]
Get:76 http://172.17.4.1/private bookworm-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:77 http://172.17.4.1/private bookworm-staging/main armhf libfreetype6 armhf 2.11.1+dfsg-1 [334 kB]
Get:78 http://172.17.4.1/private bookworm-staging/main armhf libfontconfig1 armhf 2.13.1-4.4 [331 kB]
Get:79 http://172.17.4.1/private bookworm-staging/main armhf libpixman-1-0 armhf 0.40.0-1 [463 kB]
Get:80 http://172.17.4.1/private bookworm-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:81 http://172.17.4.1/private bookworm-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:82 http://172.17.4.1/private bookworm-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:83 http://172.17.4.1/private bookworm-staging/main armhf libx11-data all 2:1.7.2-2 [311 kB]
Get:84 http://172.17.4.1/private bookworm-staging/main armhf libx11-6 armhf 2:1.7.2-2 [704 kB]
Get:85 http://172.17.4.1/private bookworm-staging/main armhf libxcb-render0 armhf 1.14-3 [110 kB]
Get:86 http://172.17.4.1/private bookworm-staging/main armhf libxcb-shm0 armhf 1.14-3 [101 kB]
Get:87 http://172.17.4.1/private bookworm-staging/main armhf libxext6 armhf 2:1.3.4-1 [48.0 kB]
Get:88 http://172.17.4.1/private bookworm-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:89 http://172.17.4.1/private bookworm-staging/main armhf libcairo2 armhf 1.16.0-5 [602 kB]
Get:90 http://172.17.4.1/private bookworm-staging/main armhf libexpat1-dev armhf 2.4.4-1 [135 kB]
Get:91 http://172.17.4.1/private bookworm-staging/main armhf libglib2.0-0 armhf 2.70.3-1 [1209 kB]
Get:92 http://172.17.4.1/private bookworm-staging/main armhf libinchi1 armhf 1.03+dfsg-4 [343 kB]
Get:93 http://172.17.4.1/private bookworm-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-8 [315 kB]
Get:94 http://172.17.4.1/private bookworm-staging/main armhf libjs-underscore all 1.13.2~dfsg-2 [116 kB]
Get:95 http://172.17.4.1/private bookworm-staging/main armhf libjs-sphinxdoc all 4.3.2-1 [139 kB]
Get:96 http://172.17.4.1/private bookworm-staging/main armhf liblapack3 armhf 3.10.0-2 [1590 kB]
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Get:98 http://172.17.4.1/private bookworm-staging/main armhf libopenbabel7 armhf 3.1.1+dfsg-6 [2775 kB]
Get:99 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9 armhf 3.9.10-1+rpi1 [1419 kB]
Get:100 http://172.17.4.1/private bookworm-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:101 http://172.17.4.1/private bookworm-staging/main armhf libpython3.9-dev armhf 3.9.10-1+rpi1 [3015 kB]
Get:102 http://172.17.4.1/private bookworm-staging/main armhf libpython3-dev armhf 3.9.7-1+b4 [22.1 kB]
Get:103 http://172.17.4.1/private bookworm-staging/main armhf libxml2-utils armhf 2.9.12+dfsg-5 [106 kB]
Get:104 http://172.17.4.1/private bookworm-staging/main armhf libxslt1.1 armhf 1.1.34-4 [218 kB]
Get:105 http://172.17.4.1/private bookworm-staging/main armhf openbabel armhf 3.1.1+dfsg-6 [128 kB]
Get:106 http://172.17.4.1/private bookworm-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:107 http://172.17.4.1/private bookworm-staging/main armhf python3.9-dev armhf 3.9.10-1+rpi1 [501 kB]
Get:108 http://172.17.4.1/private bookworm-staging/main armhf python3-dev armhf 3.9.7-1+b4 [25.3 kB]
Get:109 http://172.17.4.1/private bookworm-staging/main armhf python3-pkg-resources all 59.6.0-1.2 [196 kB]
Get:110 http://172.17.4.1/private bookworm-staging/main armhf python3-numpy armhf 1:1.21.5-1 [3437 kB]
Get:111 http://172.17.4.1/private bookworm-staging/main armhf scons all 4.0.1+dfsg-2 [559 kB]
Get:112 http://172.17.4.1/private bookworm-staging/main armhf swig4.0 armhf 4.0.2-2 [1221 kB]
Get:113 http://172.17.4.1/private bookworm-staging/main armhf swig all 4.0.2-2 [330 kB]
Get:114 http://172.17.4.1/private bookworm-staging/main armhf xsltproc armhf 1.1.34-4 [123 kB]
Get:115 http://172.17.4.1/private bookworm-staging/main armhf xmlto armhf 0.0.28-2.1 [32.1 kB]
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Setting up media-types (5.0.0) ...
Setting up libpipeline1:armhf (1.5.5-1) ...
Setting up cpp-11 (11.2.0-16+rpi1) ...
Setting up libpixman-1-0:armhf (0.40.0-1) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up bsdextrautils (2.37.3-1) ...
Setting up libicu67:armhf (67.1-7) ...
Setting up libmagic-mgc (1:5.41-2) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up libglib2.0-0:armhf (2.70.3-1) ...
No schema files found: doing nothing.
Setting up libdebhelper-perl (13.6) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libmagic1:armhf (1:5.41-2) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.41-2) ...
Setting up libgomp1:armhf (11.2.0-16+rpi1) ...
Setting up libboost-iostreams1.71.0:armhf (1.71.0-7+b1) ...
Setting up libasan6:armhf (11.2.0-16+rpi1) ...
Setting up libmaeparser1:armhf (1.2.4-1) ...
Setting up autotools-dev (20220109.1) ...
Setting up libblas3:armhf (3.10.0-2) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libexpat1-dev:armhf (2.4.4-1) ...
Setting up libx11-data (2:1.7.2-2) ...
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Setting up libpng16-16:armhf (1.6.37-3) ...
Setting up libatomic1:armhf (11.2.0-16+rpi1) ...
Setting up autopoint (0.21-4) ...
Setting up pkg-config (0.29.2-1) ...
Setting up fonts-dejavu-core (2.37-2) ...
Setting up ucf (3.0043) ...
Setting up libgfortran5:armhf (11.2.0-16+rpi1) ...
Setting up libubsan1:armhf (11.2.0-16+rpi1) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libgcc-11-dev:armhf (11.2.0-16+rpi1) ...
Setting up libmd0:armhf (1.0.4-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libmpdec3:armhf (2.5.1-2+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up sgml-base (1.30) ...
Setting up dos2unix (7.4.2-2) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-8) ...
Setting up swig4.0 (4.0.2-2) ...
Setting up libbsd0:armhf (0.11.5-1) ...
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Setting up libxml2:armhf (2.9.12+dfsg-5) ...
Setting up libcc1-0:armhf (11.2.0-16+rpi1) ...
Setting up libpython3.9-stdlib:armhf (3.9.10-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.7-1+b4) ...
Setting up libjs-underscore (1.13.2~dfsg-2) ...
Setting up libinchi1 (1.03+dfsg-4) ...
Setting up libfile-stripnondeterminism-perl (1.13.0-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.10.0-2) ...
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 (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up swig (4.0.2-2) ...
Setting up libtool (2.4.6-15) ...
Setting up libxcb-render0:armhf (1.14-3) ...
Setting up libgfortran-11-dev:armhf (11.2.0-16+rpi1) ...
Setting up fontconfig-config (2.13.1-4.4) ...
Setting up m4 (1.4.18-5) ...
Setting up libxcb-shm0:armhf (1.14-3) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libpython3.9:armhf (3.9.10-1+rpi1) ...
Setting up libfreetype6:armhf (2.11.1+dfsg-1) ...
Setting up libjs-sphinxdoc (4.3.2-1) ...
Setting up autoconf (2.71-2) ...
Setting up libstdc++-11-dev:armhf (11.2.0-16+rpi1) ...
Setting up dh-strip-nondeterminism (1.13.0-1) ...
Setting up dwz (0.14-1) ...
Setting up gcc-11 (11.2.0-16+rpi1) ...
Setting up groff-base (1.22.4-8) ...
Setting up xml-core (0.18+nmu1) ...
Setting up libxslt1.1:armhf (1.1.34-4) ...
Setting up libx11-6:armhf (2:1.7.2-2) ...
Setting up libfontconfig1:armhf (2.13.1-4.4) ...
Setting up libxml2-utils (2.9.12+dfsg-5) ...
Setting up python3.9 (3.9.10-1+rpi1) ...
Setting up automake (1:1.16.5-1.1) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up g++-11 (11.2.0-16+rpi1) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up xsltproc (1.1.34-4) ...
Setting up libxext6:armhf (2:1.3.4-1) ...
Setting up libpython3.9-dev:armhf (3.9.10-1+rpi1) ...
Setting up python3 (3.9.7-1+b4) ...
Setting up man-db (2.10.0-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:armhf (1.16.0-5) ...
Setting up dh-autoreconf (20) ...
Setting up gfortran-11 (11.2.0-16+rpi1) ...
Setting up python3.9-dev (3.9.10-1+rpi1) ...
Setting up python3-lib2to3 (3.9.10-1) ...
Setting up python3-pkg-resources (59.6.0-1.2) ...
Setting up python3-distutils (3.9.10-1) ...
Setting up dh-python (5.20220119) ...
Setting up libpython3-dev:armhf (3.9.7-1+b4) ...
Setting up libopenbabel7 (3.1.1+dfsg-6) ...
Setting up debhelper (13.6) ...
Setting up gfortran (4:11.2.0-2+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 python3-dev (3.9.7-1+b4) ...
Setting up scons (4.0.1+dfsg-2) ...
Setting up python3-numpy (1:1.21.5-1) ...
Setting up openbabel (3.1.1+dfsg-6) ...
Processing triggers for libc-bin (2.33-5+rpi1) ...
Processing triggers for sgml-base (1.30) ...
Setting up docbook-xsl (1.79.2+dfsg-1) ...
Setting up sgml-data (2.0.11+nmu1) ...
Processing triggers for sgml-base (1.30) ...
Setting up docbook-xml (4.5-11) ...
Processing triggers for sgml-base (1.30) ...
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.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.37.90.20220130-2+rpi2 dpkg-dev_1.21.1+rpi1 g++-11_11.2.0-16+rpi1 gcc-11_11.2.0-16+rpi1 libc6-dev_2.33-5+rpi1 libstdc++-11-dev_11.2.0-16+rpi1 libstdc++6_11.2.0-16+rpi1 linux-libc-dev_5.14.16-1+rpi1
Package versions: adduser_3.118 apt_2.3.15 autoconf_2.71-2 automake_1:1.16.5-1.1 autopoint_0.21-4 autotools-dev_20220109.1 base-files_12+rpi1 base-passwd_3.5.52 bash_5.1-6 binutils_2.37.90.20220130-2+rpi2 binutils-arm-linux-gnueabihf_2.37.90.20220130-2+rpi2 binutils-common_2.37.90.20220130-2+rpi2 bsdextrautils_2.37.3-1 bsdutils_1:2.37.3-1 build-essential_12.9 bzip2_1.0.8-5 coreutils_8.32-4.1 cpp_4:11.2.0-2+rpi1 cpp-11_11.2.0-16+rpi1 dash_0.5.11+git20210903+057cd650a4ed-3 debconf_1.5.79 debhelper_13.6 debianutils_4.11.2 dh-autoreconf_20 dh-python_5.20220119 dh-strip-nondeterminism_1.13.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-3 docbook-xml_4.5-11 docbook-xsl_1.79.2+dfsg-1 dos2unix_7.4.2-2 dpkg_1.21.1+rpi1 dpkg-dev_1.21.1+rpi1 dwz_0.14-1 e2fsprogs_1.46.5-2 fakeroot_1.27-1 file_1:5.41-2 findutils_4.8.0-1 fontconfig-config_2.13.1-4.4 fonts-dejavu-core_2.37-2 g++_4:11.2.0-2+rpi1 g++-11_11.2.0-16+rpi1 gcc_4:11.2.0-2+rpi1 gcc-11_11.2.0-16+rpi1 gcc-11-base_11.2.0-16+rpi1 gcc-7-base_7.5.0-6+rpi1+b2 gcc-8-base_8.4.0-7+rpi1 gcc-9-base_9.4.0-2+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran_4:11.2.0-2+rpi1 gfortran-11_11.2.0-16+rpi1 gnupg_2.2.27-3 gnupg-l10n_2.2.27-3 gnupg-utils_2.2.27-3 gpg_2.2.27-3 gpg-agent_2.2.27-3 gpg-wks-client_2.2.27-3 gpg-wks-server_2.2.27-3 gpgconf_2.2.27-3 gpgsm_2.2.27-3 gpgv_2.2.27-3 grep_3.7-1 groff-base_1.22.4-8 gzip_1.10-4 hostname_3.23 init-system-helpers_1.61 intltool-debian_0.35.0+20060710.5 libacl1_2.3.1-1 libapt-pkg6.0_2.3.15 libarchive-zip-perl_1.68-1 libasan6_11.2.0-16+rpi1 libassuan0_2.5.5-1 libatomic1_11.2.0-16+rpi1 libattr1_1:2.5.1-1 libaudit-common_1:3.0.6-1 libaudit1_1:3.0.6-1 libbinutils_2.37.90.20220130-2+rpi2 libblas3_3.10.0-2 libblkid1_2.37.3-1 libboost-iostreams1.71.0_1.71.0-7+b1 libbrotli1_1.0.9-2+b1 libbsd0_0.11.5-1 libbz2-1.0_1.0.8-5 libc-bin_2.33-5+rpi1 libc-dev-bin_2.33-5+rpi1 libc6_2.33-5+rpi1 libc6-dev_2.33-5+rpi1 libcairo2_1.16.0-5 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcc1-0_11.2.0-16+rpi1 libcom-err2_1.46.5-2 libcrypt-dev_1:4.4.27-1.1 libcrypt1_1:4.4.27-1.1 libctf-nobfd0_2.37.90.20220130-2+rpi2 libctf0_2.37.90.20220130-2+rpi2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.261 libdebhelper-perl_13.6 libdpkg-perl_1.21.1+rpi1 libelf1_0.186-1 libexpat1_2.4.4-1 libexpat1-dev_2.4.4-1 libext2fs2_1.46.5-2 libfakeroot_1.27-1 libffi8_3.4.2-4 libfile-stripnondeterminism-perl_1.13.0-1 libfontconfig1_2.13.1-4.4 libfreetype6_2.11.1+dfsg-1 libgcc-11-dev_11.2.0-16+rpi1 libgcc-s1_11.2.0-16+rpi1 libgcrypt20_1.9.4-5 libgdbm-compat4_1.23-1 libgdbm6_1.23-1 libgfortran-11-dev_11.2.0-16+rpi1 libgfortran5_11.2.0-16+rpi1 libglib2.0-0_2.70.3-1 libgmp10_2:6.2.1+dfsg-3 libgnutls30_3.7.3-4 libgomp1_11.2.0-16+rpi1 libgpg-error0_1.43-3 libgssapi-krb5-2_1.18.3-7 libhogweed6_3.7.3-1 libicu67_67.1-7 libidn2-0_2.3.2-2 libinchi1_1.03+dfsg-4 libisl23_0.24-2 libjs-jquery_3.5.1+dfsg+~3.5.5-8 libjs-sphinxdoc_4.3.2-1 libjs-underscore_1.13.2~dfsg-2 libk5crypto3_1.18.3-7 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-7 libkrb5support0_1.18.3-7 libksba8_1.6.0-2 liblapack3_3.10.0-2 libldap-2.4-2_2.4.59+dfsg-1 liblz4-1_1.9.3-2 liblzma5_5.2.5-2 libmaeparser1_1.2.4-1 libmagic-mgc_1:5.41-2 libmagic1_1:5.41-2 libmd0_1.0.4-1 libmount1_2.37.3-1 libmpc3_1.2.1-1 libmpdec3_2.5.1-2+rpi1 libmpfr6_4.1.0-3 libncursesw6_6.3-2 libnettle8_3.7.3-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libopenbabel7_3.1.1+dfsg-6 libp11-kit0_0.24.0-6 libpam-modules_1.4.0-11 libpam-modules-bin_1.4.0-11 libpam-runtime_1.4.0-11 libpam0g_1.4.0-11 libpcre2-8-0_10.39-3 libpcre3_2:8.39-13 libperl5.32_5.32.1-6 libperl5.34_5.34.0-3 libpipeline1_1.5.5-1 libpixman-1-0_0.40.0-1 libpng16-16_1.6.37-3 libpython3-dev_3.9.7-1+b4 libpython3-stdlib_3.9.7-1+b4 libpython3.9_3.9.10-1+rpi1 libpython3.9-dev_3.9.10-1+rpi1 libpython3.9-minimal_3.9.10-1+rpi1 libpython3.9-stdlib_3.9.10-1+rpi1 libreadline8_8.1.2-1 libsasl2-2_2.1.27+dfsg2-3 libsasl2-modules-db_2.1.27+dfsg2-3 libseccomp2_2.5.3-2+rpi1 libselinux1_3.3-1 libsemanage-common_3.3-1 libsemanage2_3.3-1 libsepol1_3.1-1 libsepol2_3.3-1 libsigsegv2_2.14-1 libsmartcols1_2.37.3-1 libsqlite3-0_3.37.2-2 libss2_1.46.5-2 libssl1.1_1.1.1m-1 libstdc++-11-dev_11.2.0-16+rpi1 libstdc++6_11.2.0-16+rpi1 libsub-override-perl_0.09-2 libsystemd0_250.3-2+rpi1 libtasn1-6_4.18.0-4 libtinfo6_6.3-2 libtirpc-common_1.3.2-2 libtirpc-dev_1.3.2-2 libtirpc3_1.3.2-2 libtool_2.4.6-15 libubsan1_11.2.0-16+rpi1 libuchardet0_0.0.7-1 libudev1_250.3-2+rpi1 libunistring2_1.0-1 libuuid1_2.37.3-1 libx11-6_2:1.7.2-2 libx11-data_2:1.7.2-2 libxau6_1:1.0.9-1 libxcb-render0_1.14-3 libxcb-shm0_1.14-3 libxcb1_1.14-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.4-1 libxml2_2.9.12+dfsg-5 libxml2-utils_2.9.12+dfsg-5 libxrender1_1:0.9.10-1 libxslt1.1_1.1.34-4 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-3+rpi1 linux-libc-dev_5.14.16-1+rpi1 login_1:4.11.1+dfsg1-1 logsave_1.46.5-2 lsb-base_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4.1 man-db_2.10.0-2 mawk_1.3.4.20200120-3 media-types_5.0.0 mount_2.37.3-1 ncurses-base_6.3-2 ncurses-bin_6.3-2 netbase_6.3 openbabel_3.1.1+dfsg-6 passwd_1:4.11.1+dfsg1-1 patch_2.7.6-7 perl_5.34.0-3 perl-base_5.34.0-3 perl-modules-5.32_5.32.1-6 perl-modules-5.34_5.34.0-3 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21+nmu1 python3_3.9.7-1+b4 python3-dev_3.9.7-1+b4 python3-distutils_3.9.10-1 python3-lib2to3_3.9.10-1 python3-minimal_3.9.7-1+b4 python3-numpy_1:1.21.5-1 python3-pkg-resources_59.6.0-1.2 python3.9_3.9.10-1+rpi1 python3.9-dev_3.9.10-1+rpi1 python3.9-minimal_3.9.10-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1.2-1 rpcsvc-proto_1.4.2-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pdb2pqr-dummy_0.invalid.0 scons_4.0.1+dfsg-2 sed_4.8-1 sensible-utils_0.0.17 sgml-base_1.30 sgml-data_2.0.11+nmu1 swig_4.0.2-2 swig4.0_4.0.2-2 sysvinit-utils_3.01-1 tar_1.34+dfsg-1 tzdata_2021e-1 ucf_3.0043 util-linux_2.37.3-1 xml-core_0.18+nmu1 xmlto_0.0.28-2.1 xsltproc_1.1.34-4 xz-utils_5.2.5-2 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 '/tmp/dpkg-verify-sig.6eAJdH4V/trustedkeys.kbx': General error
gpgv: Signature made Thu Feb 10 14:37:03 2022 UTC
gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287
gpgv: issuer "merkys@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: cannot verify signature ./pdb2pqr_2.1.1+dfsg-8.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-8.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
dpkg-source: info: applying reproducible-build.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=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bookworm-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bookworm-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bookworm-staging-armhf-sbuild-1b47db7a-f477-4290-a7ca-276501f16c21
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-8
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
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 binary-arch
dh binary-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/python3.9 -I/usr/include/arm-linux-gnueabihf/python3.9 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/substruct/Algorithms.cpp
In file included from /usr/include/python3.9/numpy/ndarraytypes.h:1969,
from /usr/include/python3.9/numpy/ndarrayobject.h:12,
from /usr/include/python3.9/numpy/arrayobject.h:4,
from pdb2pka/substruct/Algorithms.cpp:43:
/usr/include/python3.9/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-39-arm-linux-gnueabihf.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib/arm-linux-gnueabihf
g++ -o pdb2pka/pMC_mult.os -c -g -fPIC -I/usr/include/python3.9 -I/usr/include/arm-linux-gnueabihf/python3.9 -I/usr/include/python3.9 -I/usr/lib/python3/dist-packages/numpy/core/include pdb2pka/pMC_mult.cpp
In file included from /usr/include/c++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/stl_vector.h:558:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
558 | std::__uninitialized_copy_a(__x.begin(), __x.end(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
559 | this->_M_impl._M_start,
| ~~~~~~~~~~~~~~~~~~~~~~~
560 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
331 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:333:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
333 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/11/bits/vector.tcc:121:28: 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++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
126 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
148 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
151 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:108:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
108 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:108:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:110:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
110 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
611 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:620:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
619 | return std::__copy_move_a<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
620 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:61,
from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/cpp_type_traits.h:560:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
560 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/bits/stl_algobase.h: In function '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/11/bits/stl_algobase.h:527:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
527 | __copy_move_a(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h:527:5: 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++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/bits/char_traits.h:39,
from /usr/include/c++/11/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/11/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++/11/bits/stl_iterator.h:1257:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1257 | __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
| ^~~~~~~~~~~~
g++ -o pdb2pka/pMC_mult_wrap.os -c -g -fPIC -I/usr/include/python3.9 -I/usr/include/arm-linux-gnueabihf/python3.9 -I/usr/include/python3.9 -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:4847:44: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
4847 | 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:4847:167: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
4847 | 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:4848:44: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
4848 | 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:4848:44: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp:4848:206: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
4848 | 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:4849:44: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
4849 | 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:4849:212: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
4849 | 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:4850:17: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
4850 | 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:4850:213: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
4850 | 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:8847:50: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
8847 | 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:8897:50: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
8897 | 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:9288:51: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
9288 | 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:9341:42: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
9341 | std_vector_Sl_double_Sg__insert__SWIG_1(arg1,arg2,arg3,(double const &)*arg4);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:558:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
558 | std::__uninitialized_copy_a(__x.begin(), __x.end(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
559 | this->_M_impl._M_start,
| ~~~~~~~~~~~~~~~~~~~~~~~
560 | _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:4163:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4163 | return new SwigPyIteratorClosed_T<OutIter>(current, begin, end, seq);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4163:12: 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:3782:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
3782 | 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:3828:33: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
3828 | self->insert(std::copy(is.begin(), isit, sb), isit, is.end());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:3828:23: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
3828 | self->insert(std::copy(is.begin(), isit, sb), isit, is.end());
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:3828:23: 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:3835:22: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
3835 | self->erase(sb,se);
| ~~~~~~~~~~~^~~~~~~
pdb2pka/pMC_mult_wrap.cpp:3838:23: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
3838 | self->insert(sb, is.begin(), is.end());
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:3838:23: 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:3887:20: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
3887 | self->erase(sb,se);
| ~~~~~~~~~~~^~~~~~~
pdb2pka/pMC_mult_wrap.cpp:3892:27: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
3892 | it = self->erase(it);
| ~~~~~~~~~~~^~~~
pdb2pka/pMC_mult_wrap.cpp:3904:33: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
3904 | it = typename Sequence::reverse_iterator(self->erase((++it).base()));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:3904:33: 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:3758:15: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
3758 | seq->erase(position);
| ~~~~~~~~~~^~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1198:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:1430:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
1430 | erase(const_iterator __position)
| ^~~~~
/usr/include/c++/11/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:1457:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
1457 | erase(const_iterator __first, const_iterator __last)
| ^~~~~
/usr/include/c++/11/bits/stl_vector.h:1457:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1461:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1461 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg));
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:130:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
130 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:154:26: 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++/11/bits/vector.tcc:161:26: 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++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1335:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
1335 | insert(const_iterator __position, size_type __n, const value_type& __x)
| ^~~~~~
/usr/include/c++/11/bits/stl_vector.h:1338:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1338 | _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:4177:12: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
4177 | return new SwigPyIteratorOpen_T<OutIter>(current, seq);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:848:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
848 | { return reverse_iterator(end()); }
| ^
/usr/include/c++/11/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++/11/bits/stl_vector.h:866:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
866 | { return reverse_iterator(begin()); }
| ^
/usr/include/c++/11/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++/11/bits/stl_vector.h:960:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:226:51: 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(),
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
227 | __x.end());
| ~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:238:28: 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++/11/bits/vector.tcc:238:28: 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++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
331 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:333:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
333 | { 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:4133:5: 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
4133 | SwigPyIteratorClosed_T(out_iterator curr, out_iterator first, out_iterator last, PyObject *seq)
| ^~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4133:5: 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:4133:5: 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:4134:93: 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
4134 | : SwigPyForwardIteratorClosed_T<OutIterator,ValueType,FromOper>(curr, first, last, seq)
| ^
pdb2pka/pMC_mult_wrap.cpp:4134:93: 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++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:653:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
653 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/11/bits/stl_vector.h:653:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:657:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
657 | _M_range_initialize(__first, __last,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
658 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_vector.h:857:44: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
857 | { return const_reverse_iterator(end()); }
| ^
In file included from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
611 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:620:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
619 | return std::__copy_move_a<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
620 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1379:9: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
1379 | insert(const_iterator __position, _InputIterator __first,
| ^~~~~~
/usr/include/c++/11/bits/stl_vector.h:1379:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1379:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1383:29: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1383 | _M_insert_dispatch(begin() + __offset,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
1384 | __first, __last, __false_type());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1383:29: 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++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_iterator.h: In constructor 'constexpr 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++/11/bits/stl_iterator.h:183:7: note: parameter passing for argument of type 'std::reverse_iterator<__gnu_cxx::__normal_iterator<double*, std::vector<double> > >::iterator_type' changed in GCC 7.1
183 | reverse_iterator(iterator_type __x) : current(__x) { }
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/vector.tcc:175:9: 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++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
184 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:184:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/vector.tcc:190:13: 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++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:395:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
395 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' 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:4059:5: 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
4059 | SwigPyIteratorOpen_T(out_iterator curr, PyObject *seq)
| ^~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4060:59: 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
4060 | : SwigPyForwardIteratorOpen_T<OutIterator>(curr, seq)
| ^
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:267:20: 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++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1508:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1508 | _M_allocate_and_copy(size_type __n,
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1508:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1514:42: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1514 | std::__uninitialized_copy_a(__first, __last, __result,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1515 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/ext/alloc_traits.h:34,
from /usr/include/c++/11/bits/basic_string.h:40,
from /usr/include/c++/11/string:55,
from /usr/include/c++/11/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/11/bits/alloc_traits.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++/11/bits/alloc_traits.h:851:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
851 | _Destroy(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~
/usr/include/c++/11/bits/alloc_traits.h:851:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/alloc_traits.h:854:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
854 | _Destroy(__first, __last);
| ~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
126 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
148 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
151 | __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:4085:5: 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
4085 | SwigPyForwardIteratorClosed_T(out_iterator curr, out_iterator first, out_iterator last, PyObject *seq)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4085:5: 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:4085:5: 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:4086:73: 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
4086 | : SwigPyIterator_T<OutIterator>(curr, seq), begin(first), end(last)
| ^
In file included from /usr/include/c++/11/bits/stl_algobase.h:66,
from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_iterator_base_funcs.h: In function 'constexpr typename std::iterator_traits< <template-parameter-1-1> >::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/11/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++/11/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++/11/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++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1577:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1577 | _M_range_initialize(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1577:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1580:46: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1580 | const size_type __n = std::distance(__first, __last);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1585:40: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1585 | std::__uninitialized_copy_a(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1586 | this->_M_impl._M_start,
| ~~~~~~~~~~~~~~~~~~~~~~~
1587 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_iterator.h: In constructor 'constexpr 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++/11/bits/stl_iterator.h:183:7: note: parameter passing for argument of type 'std::reverse_iterator<__gnu_cxx::__normal_iterator<const double*, std::vector<double> > >::iterator_type' changed in GCC 7.1
183 | reverse_iterator(iterator_type __x) : current(__x) { }
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/cmath:42,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/cpp_type_traits.h:560:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
560 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_algobase.h: In function '_OI std::__copy_move_a(_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++/11/bits/stl_algobase.h:527:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
527 | __copy_move_a(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h:527:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:527:5: 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++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1662:9: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
1662 | _M_insert_dispatch(iterator __pos, _InputIterator __first,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1662:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1662:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_vector.h:1665:26: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_vector.h:1665:26: 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++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/stl_algobase.h:644:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
644 | move(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/11/bits/stl_algobase.h:644:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:644:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:652:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
652 | return std::__copy_move_a<true>(std::__miter_base(__first),
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
653 | std::__miter_base(__last), __result);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:341:41: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
341 | return std::__uninitialized_copy_a(_GLIBCXX_MAKE_MOVE_ITERATOR(__first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
342 | _GLIBCXX_MAKE_MOVE_ITERATOR(__last),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
343 | __result, __alloc);
| ~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:355:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
354 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
355 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
356 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __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:4023:5: 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
4023 | SwigPyForwardIteratorOpen_T(out_iterator curr, PyObject *seq)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
pdb2pka/pMC_mult_wrap.cpp:4024:48: 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
4024 | : SwigPyIterator_T<OutIterator>(curr, seq)
| ^
In file included from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/stl_algobase.h:992:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
992 | fill(_ForwardIterator __first, _ForwardIterator __last, const _Tp& __value)
| ^~~~
/usr/include/c++/11/bits/stl_algobase.h:992:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:999:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
999 | std::__fill_a(__first, __last, __value);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/alloc_traits.h:33,
from /usr/include/c++/11/ext/alloc_traits.h:34,
from /usr/include/c++/11/bits/basic_string.h:40,
from /usr/include/c++/11/string:55,
from /usr/include/c++/11/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/11/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/11/bits/stl_construct.h:182:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
182 | _Destroy(_ForwardIterator __first, _ForwardIterator __last)
| ^~~~~~~~
/usr/include/c++/11/bits/stl_construct.h:182:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_construct.h:196:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
195 | std::_Destroy_aux<__has_trivial_destructor(_Value_type)>::
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
196 | __destroy(__first, __last);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:108:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
108 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:108:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:110:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
110 | { 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:3965:5: 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
3965 | SwigPyIterator_T(out_iterator curr, PyObject *seq)
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:66,
from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_iterator_base_funcs.h: In function 'constexpr typename std::iterator_traits< <template-parameter-1-1> >::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++/11/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++/11/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++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/stl_iterator.h:1257:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1257 | __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
| ^~~~~~~~~~~~
/usr/include/c++/11/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++/11/bits/stl_iterator.h:1257:5: 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++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/stl_algobase.h:328:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
328 | __niter_wrap(_From __from, _To __res)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/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++/11/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++/11/bits/vector.tcc:727:48: 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++/11/bits/vector.tcc:744:30: 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++/11/bits/vector.tcc:751:48: 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++/11/bits/vector.tcc:762:30: 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++/11/bits/vector.tcc:778:52: 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++/11/cmath:42,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/cpp_type_traits.h:560:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
560 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_algobase.h: In function '_OI std::__copy_move_a(_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++/11/bits/stl_algobase.h:527:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
527 | __copy_move_a(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h:527:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:527:5: 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++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
331 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:331:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:333:37: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
333 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
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:4462:18: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
4462 | seq->insert(seq->end(),(value_type)(*it));
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_algobase.h: In function 'void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double]':
/usr/include/c++/11/bits/stl_algobase.h:968:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
968 | __fill_a(_FIte __first, _FIte __last, const _Tp& __value)
| ^~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h:968:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:969:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
969 | { std::__fill_a1(__first, __last, __value); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/alloc_traits.h:33,
from /usr/include/c++/11/ext/alloc_traits.h:34,
from /usr/include/c++/11/bits/basic_string.h:40,
from /usr/include/c++/11/string:55,
from /usr/include/c++/11/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/11/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++/11/bits/stl_construct.h:172:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
172 | __destroy(_ForwardIterator, _ForwardIterator) { }
| ^~~~~~~~~
/usr/include/c++/11/bits/stl_construct.h:172:9: 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++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
611 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h:620:14: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
619 | return std::__copy_move_a<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
620 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/11/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
126 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:126:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:151:22: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
148 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
150 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
151 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_vector.h:1293:7: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
1293 | insert(const_iterator __position, value_type&& __x)
| ^~~~~~
/usr/include/c++/11/bits/stl_vector.h:1294:30: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
1294 | { return _M_insert_rval(__position, std::move(__x)); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_algobase.h: In function 'void std::__fill_a1(__gnu_cxx::__normal_iterator<_Iterator, _Container>, __gnu_cxx::__normal_iterator<_Iterator, _Container>, const _Tp&) [with _Ite = double*; _Cont = std::vector<double>; _Tp = double]':
/usr/include/c++/11/bits/stl_algobase.h:950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
950 | __fill_a1(::__gnu_cxx::__normal_iterator<_Ite, _Cont> __first,
| ^~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h:950:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/11/bits/stl_algobase.h: In function '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >; _OI = double*]':
/usr/include/c++/11/bits/stl_algobase.h:527:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
527 | __copy_move_a(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_algobase.h:527:5: 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++/11/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/stl_uninitialized.h:108:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
108 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/11/bits/stl_uninitialized.h:108:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/11/bits/stl_uninitialized.h:110:27: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
110 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:340:5: note: parameter passing for argument of type 'std::vector<double>::const_iterator' changed in GCC 7.1
340 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/11/bits/vector.tcc:354:24: 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++/11/bits/vector.tcc:356:26: 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++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
611 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/11/bits/stl_algobase.h:611:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/11/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/11/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++/11/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:67,
from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/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++/11/bits/stl_iterator.h:2354:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
2354 | __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:3990:29: note: parameter passing for argument of type 'const __gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
3990 | return std::distance(current, iters->get_current());
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/11/bits/stl_algobase.h:66,
from /usr/include/c++/11/bits/specfun.h:45,
from /usr/include/c++/11/cmath:1935,
from /usr/include/c++/11/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:50,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/11/bits/stl_iterator_base_funcs.h: In function 'constexpr typename std::iterator_traits< <template-parameter-1-1> >::difference_type std::distance(_InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/11/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++/11/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++/11/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++/11/bits/stl_iterator_base_funcs.h: In function 'constexpr typename std::iterator_traits< <template-parameter-1-1> >::difference_type std::__distance(_RandomAccessIterator, _RandomAccessIterator, std::random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/11/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++/11/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-39-arm-linux-gnueabihf.so -Wl,-z,relro -Wl,-z,now -shared pdb2pka/pMC_mult.os pdb2pka/pMC_mult_wrap.os -L/usr/lib/arm-linux-gnueabihf
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-39-arm-linux-gnueabihf.so', 'pdb2pka/_pMC_mult.cpython-39-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
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-39-arm-linux-gnueabihf.so usr/share/pdb2pqr/pdb2pka/_pMC_mult.so
dh_link -a usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-39-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-8_armhf.deb'.
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-8_armhf.deb'.
dpkg-genbuildinfo --build=any -O../pdb2pqr_2.1.1+dfsg-8_armhf.buildinfo
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> -O../pdb2pqr_2.1.1+dfsg-8_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 2022-02-13T13:16:26Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pdb2pqr_2.1.1+dfsg-8_armhf.changes:
-----------------------------------
Format: 1.8
Date: Thu, 10 Feb 2022 09:28:48 -0500
Source: pdb2pqr
Binary: pdb2pqr pdb2pqr-dbgsym
Architecture: armhf
Version: 2.1.1+dfsg-8
Distribution: bookworm-staging
Urgency: medium
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Andrius Merkys <merkys@debian.org>
Description:
pdb2pqr - Preparation of protein structures for electrostatics calculations
Changes:
pdb2pqr (2.1.1+dfsg-8) unstable; urgency=medium
.
* Team upload.
* Add an autopkgtest for propka.
* Fix Python problem causing crashes in propka.
* Source moved to GitHub.
Checksums-Sha1:
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b07442361b7dd0ae3335ac72242be3512700cfc1 7168 pdb2pqr_2.1.1+dfsg-8_armhf.buildinfo
b4f54e6b19681fb17acdc0f1a8655de96628b21a 368524 pdb2pqr_2.1.1+dfsg-8_armhf.deb
Checksums-Sha256:
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46851a6650dbf438515d506ff8db0c1a3003e27a370a28f86a7dd071bc57707e 7168 pdb2pqr_2.1.1+dfsg-8_armhf.buildinfo
87dcec542dabf7a5cd3b371fbabd8ac3d47260b46818566ac4886cb7a180f379 368524 pdb2pqr_2.1.1+dfsg-8_armhf.deb
Files:
1d5c6219a640802851bc84fc44c90e0c 290456 debug optional pdb2pqr-dbgsym_2.1.1+dfsg-8_armhf.deb
b0693d5fe991705669009a3b12c3d989 7168 science optional pdb2pqr_2.1.1+dfsg-8_armhf.buildinfo
67d315fc337fa6909aa267316deb5dee 368524 science optional pdb2pqr_2.1.1+dfsg-8_armhf.deb
+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pdb2pqr-dbgsym_2.1.1+dfsg-8_armhf.deb
-------------------------------------
new Debian package, version 2.0.
size 290456 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-8
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 514
Depends: pdb2pqr (= 2.1.1+dfsg-8)
Section: debug
Priority: optional
Description: debug symbols for pdb2pqr
Build-Ids: 430f68ba8dd2d497fd437b80e0671e4013fcef4a daaae9db3e65d63059db44b17a55bb7b600792c8
drwxr-xr-x root/root 0 2022-02-10 14:28 ./
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/debug/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/debug/.build-id/43/
-rw-r--r-- root/root 15756 2022-02-10 14:28 ./usr/lib/debug/.build-id/43/0f68ba8dd2d497fd437b80e0671e4013fcef4a.debug
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/debug/.build-id/da/
-rw-r--r-- root/root 484536 2022-02-10 14:28 ./usr/lib/debug/.build-id/da/aae9db3e65d63059db44b17a55bb7b600792c8.debug
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 11168 2022-02-10 14:28 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/pdb2pqr.debug
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/doc/
lrwxrwxrwx root/root 0 2022-02-10 14:28 ./usr/share/doc/pdb2pqr-dbgsym -> pdb2pqr
pdb2pqr_2.1.1+dfsg-8_armhf.deb
------------------------------
new Debian package, version 2.0.
size 368524 bytes: control archive=4784 bytes.
1366 bytes, 28 lines control
9687 bytes, 130 lines md5sums
287 bytes, 12 lines * postinst #!/bin/sh
400 bytes, 12 lines * prerm #!/bin/sh
Package: pdb2pqr
Version: 2.1.1+dfsg-8
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2829
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 11), python3 (<< 3.10), python3 (>= 3.9~), python3:any, python3-numpy, python3-networkx
Suggests: apbs
Enhances: autodocktools
Replaces: propka
Provides: propka
Section: science
Priority: optional
Homepage: https://www.poissonboltzmann.org
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 2022-02-10 14:28 ./
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/bin/
lrwxrwxrwx root/root 0 2022-02-10 14:28 ./usr/bin/pdb2pqr -> ../share/pdb2pqr/pdb2pqr.py
lrwxrwxrwx root/root 0 2022-02-10 14:28 ./usr/bin/propka -> ../share/pdb2pqr/propka30/propka.py
lrwxrwxrwx root/root 0 2022-02-10 14:28 ./usr/bin/psize -> ../share/pdb2pqr/src/psize.py
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/pdb2pqr/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/pdb2pqr/pdb2pka/
-rw-r--r-- root/root 566228 2022-02-10 14:28 ./usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-39-arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/lib/pdb2pqr/pdb2pka/substruct/
-rw-r--r-- root/root 14620 2022-02-10 14:28 ./usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-39-arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/doc/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./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 2022-02-10 13:59 ./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 2670 2022-02-10 14:28 ./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 2022-02-10 13:59 ./usr/share/doc/pdb2pqr/copyright
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/man/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/man/man1/
-rw-r--r-- root/root 2082 2022-02-10 14:28 ./usr/share/man/man1/pdb2pqr.1.gz
-rw-r--r-- root/root 1044 2022-02-10 14:28 ./usr/share/man/man1/propka.1.gz
-rw-r--r-- root/root 1252 2022-02-10 14:28 ./usr/share/man/man1/psize.1.gz
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/pdb2pqr/
drwxr-xr-x root/root 0 2022-02-10 14:28 ./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 2022-02-10 14:28 ./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 2022-02-10 14:28 ./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 2022-02-10 14:28 ./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 2022-02-10 14:28 ./usr/share/pdb2pqr/extensions/resinter.py
-rw-r--r-- root/root 3139 2022-02-10 14:28 ./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 2022-02-10 14:28 ./usr/share/pdb2pqr/main.py
-rw-r--r-- root/root 28310 2022-02-10 14:28 ./usr/share/pdb2pqr/main_cgi.py
drwxr-xr-x root/root 0 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/
-rw-r--r-- root/root 29181 2022-02-10 14:28 ./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 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/_pMC_mult.so -> ../../../lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-39-arm-linux-gnueabihf.so
-rw-r--r-- root/root 15131 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/apbs.py
-rw-r--r-- root/root 3539 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/charge_mon.py
-rw-r--r-- root/root 8208 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/example.py
drwxr-xr-x root/root 0 2022-02-10 14:28 ./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 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/graph_cut/create_titration_output.py
-rw-r--r-- root/root 4365 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/graph_cut/graph.py
-rw-r--r-- root/root 36927 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/graph_cut/protein_complex.py
-rw-r--r-- root/root 8380 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/graph_cut/titration_curve.py
-rw-r--r-- root/root 4060 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/graph_cut/uncertainty.py
-rw-r--r-- root/root 4046 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/graph_cut/utils.py
-rw-r--r-- root/root 11732 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/inputgen_pKa.py
-rw-r--r-- root/root 29224 2022-02-10 14:28 ./usr/share/pdb2pqr/pdb2pka/ligand_topology.py
drwxr-xr-x root/root 0 2022-02-10 14:28 ./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 2022-02-10 14:28 ./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 2022-02-10 14:28 ./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
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+------------------------------------------------------------------------------+
| Post Build |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Cleanup |
+------------------------------------------------------------------------------+
Purging /<<BUILDDIR>>
Not cleaning session: cloned chroot in use
+------------------------------------------------------------------------------+
| Summary |
+------------------------------------------------------------------------------+
Build Architecture: armhf
Build-Space: 56516
Build-Time: 124
Distribution: bookworm-staging
Host Architecture: armhf
Install-Time: 1020
Job: pdb2pqr_2.1.1+dfsg-8
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 1202
Source-Version: 2.1.1+dfsg-8
Space: 56516
Status: successful
Version: 2.1.1+dfsg-8
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Finished at 2022-02-13T13:16:26Z
Build needed 00:20:02, 56516k disc space