pdb2pqr →
2.1.1+dfsg-7+b1 →
armhf → 2020-12-07 21:42:09
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on bm-wb-01
+==============================================================================+
| pdb2pqr 2.1.1+dfsg-7+b1 (armhf) Mon, 07 Dec 2020 21:19:10 +0000 |
+==============================================================================+
Package: pdb2pqr
Version: 2.1.1+dfsg-7+b1
Source Version: 2.1.1+dfsg-7
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/run/schroot/mount/bullseye-staging-armhf-sbuild-90002195-3678-4524-a2c0-a9e621e56f7b' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [11.9 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [12.9 MB]
Fetched 24.9 MB in 27s (938 kB/s)
Reading package lists...
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'pdb2pqr' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/med-team/pdb2pqr.git
Please use:
git clone https://salsa.debian.org/med-team/pdb2pqr.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 5261 kB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-7 (dsc) [2310 B]
Get:2 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-7 (tar) [5191 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main pdb2pqr 2.1.1+dfsg-7 (diff) [67.5 kB]
Fetched 5261 kB in 1s (6531 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/pdb2pqr-HLixh1/pdb2pqr-2.1.1+dfsg' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/pdb2pqr-HLixh1' 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-CSTR1R/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-CSTR1R/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-CSTR1R/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-CSTR1R/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Packages [434 B]
Fetched 2110 B in 1s (2347 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-CSTR1R/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
bsdextrautils krb5-locales libalgorithm-diff-perl libalgorithm-merge-perl
libpam-cap netbase 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 67 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.1 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12798 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) ...
+------------------------------------------------------------------------------+
| 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-CSTR1R/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-CSTR1R/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Release.gpg [370 B]
Ign:3 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Release.gpg
Get:4 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Sources [567 B]
Get:5 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Packages [650 B]
Fetched 2550 B in 1s (3431 B/s)
Reading package lists...
W: copy:///<<BUILDDIR>>/resolver-CSTR1R/apt_archive/./Release.gpg: The key(s) in the keyring /etc/apt/trusted.gpg.d/sbuild-build-depends-archive.gpg are ignored as the file is not readable by user '_apt' executing apt-key.
W: GPG error: copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 35506D9A48F77B2E
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:
krb5-locales libalgorithm-diff-perl libalgorithm-merge-perl libisl22
libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev cpp-10 debhelper dh-autoreconf
dh-python dh-strip-nondeterminism docbook-xml docbook-xsl dos2unix dwz file
fontconfig-config fonts-dejavu-core g++-10 gcc-10 gcc-10-base gettext
gettext-base gfortran gfortran-10 groff-base intltool-debian
libarchive-zip-perl libasan6 libatomic1 libblas3 libbrotli1 libbsd0
libcairo2 libcc1-0 libcroco3 libdebhelper-perl libelf1 libexpat1
libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgcc-10-dev libgcc-s1 libgfortran-10-dev libgfortran5 libglib2.0-0
libgomp1 libicu67 libinchi1 libisl23 liblapack3 libmaeparser1 libmagic-mgc
libmagic1 libopenbabel7 libpipeline1 libpixman-1-0 libpng16-16
libpython3-dev libpython3-stdlib libpython3.8-minimal libpython3.8-stdlib
libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib
libsigsegv2 libstdc++-10-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 mailcap man-db media-types mime-support openbabel pkg-config
po-debconf python3 python3-dev python3-distutils python3-lib2to3
python3-minimal python3-numpy python3-pkg-resources python3.8
python3.8-minimal 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-10-locales dh-make docbook
docbook-dsssl docbook-defguide dbtoepub docbook-xsl-doc-html
| docbook-xsl-doc-pdf | docbook-xsl-doc-text | docbook-xsl-doc
docbook-xsl-saxon fop libsaxon-java libxalan2-java libxslthl-java xalan
gcc-10-doc gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc
gfortran-10-doc libcoarrays-dev groff libstdc++-10-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-numpy-dbg
python3-setuptools python3.8-venv python3.8-doc binfmt-support
python3.9-venv python3.9-doc sgml-base-doc perlsgml w3-recs opensp swig-doc
swig-examples swig4.0-examples swig4.0-doc w3m | lynx-cur | links
texlive-htmlxml
Recommended packages:
curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info
xdg-user-dirs libltdl-dev libmail-sendmail-perl dblatex | fop libpaper-utils
zip
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev 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-10 groff-base intltool-debian libarchive-zip-perl libblas3
libbrotli1 libbsd0 libcairo2 libcroco3 libdebhelper-perl libelf1 libexpat1
libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1 libfreetype6
libgfortran-10-dev libgfortran5 libglib2.0-0 libicu67 libinchi1 libisl23
liblapack3 libmaeparser1 libmagic-mgc libmagic1 libopenbabel7 libpipeline1
libpixman-1-0 libpng16-16 libpython3-dev libpython3-stdlib
libpython3.8-minimal libpython3.8-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
mailcap man-db media-types mime-support openbabel pkg-config po-debconf
python3 python3-dev python3-distutils python3-lib2to3 python3-minimal
python3-numpy python3-pkg-resources python3.8 python3.8-minimal 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-10 g++-10 gcc-10 gcc-10-base libasan6 libatomic1 libcc1-0 libgcc-10-dev
libgcc-s1 libgomp1 libstdc++-10-dev libstdc++6 libubsan1
13 upgraded, 103 newly installed, 0 to remove and 54 not upgraded.
Need to get 221 MB of archives.
After this operation, 702 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-CSTR1R/apt_archive ./ sbuild-build-depends-pdb2pqr-dummy 0.invalid.0 [932 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libubsan1 armhf 10.2.0-19+rpi1 [115 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf gcc-10-base armhf 10.2.0-19+rpi1 [200 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libgcc-s1 armhf 10.2.0-19+rpi1 [36.2 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf libgomp1 armhf 10.2.0-19+rpi1 [83.7 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libatomic1 armhf 10.2.0-19+rpi1 [8180 B]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libasan6 armhf 10.2.0-19+rpi1 [300 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf libisl23 armhf 0.23-1 [497 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf cpp-10 armhf 10.2.0-19+rpi1 [38.5 MB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf libcc1-0 armhf 10.2.0-19+rpi1 [38.4 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf g++-10 armhf 10.2.0-19+rpi1 [41.4 MB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf gcc-10 armhf 10.2.0-19+rpi1 [44.4 MB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf libgcc-10-dev armhf 10.2.0-19+rpi1 [682 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libstdc++-10-dev armhf 10.2.0-19+rpi1 [1751 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf libstdc++6 armhf 10.2.0-19+rpi1 [409 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-5 [783 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.3-2 [1269 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.0-5+rpi1 [788 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-1 [73.3 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.0-5+rpi1 [1628 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.0-4 [37.8 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf media-types all 1.0.1 [18.2 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf mailcap all 3.67 [31.3 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf mime-support all 3.66 [10.9 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.0-5+rpi1 [1654 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.0-5+rpi1 [455 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.0-4 [21.0 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.0-4 [64.1 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-minimal armhf 3.8.6-1 [752 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf python3.8-minimal armhf 3.8.6-1 [1552 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf sgml-base all 1.30 [15.1 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.38-5 [262 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.38-5 [113 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.38-5 [67.0 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.19.8.1-10 [117 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf ucf all 3.0043 [74.0 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.12-2 [32.3 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-4 [185 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-11.1 [341 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1 [77.0 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.2-4 [801 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.19.8.1-10 [435 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-14 [513 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 19 [16.9 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.2.1 [188 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.9.0-1 [25.5 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.9.0-1 [15.2 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.182-1 [162 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13-5 [142 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libglib2.0-0 armhf 2.66.3-2 [1178 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-4 [8289 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libcroco3 armhf 0.6.13-1 [133 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.19.8.1-10 [1219 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21 [248 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.2.1 [1007 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf python3-lib2to3 all 3.8.6-1 [78.4 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf python3-distutils all 3.8.6-1 [145 kB]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf dh-python all 4.20201102 [99.3 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf xml-core all 0.18+nmu1 [23.8 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf sgml-data all 2.0.11 [179 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf docbook-xml all 4.5-9 [84.4 kB]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf docbook-xsl all 1.79.2+dfsg-1 [1237 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf dos2unix armhf 7.4.1-1 [387 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf fonts-dejavu-core all 2.37-2 [1069 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf fontconfig-config all 2.13.1-4.2 [281 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.0-19+rpi1 [231 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-10-dev armhf 10.2.0-19+rpi1 [278 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf gfortran-10 armhf 10.2.0-19+rpi1 [40.0 MB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:10.2.0-1+rpi1 [1428 B]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.10.0-1 [112 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libpng16-16 armhf 1.6.37-3 [276 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libfreetype6 armhf 2.10.2+dfsg-4 [345 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libfontconfig1 armhf 2.13.1-4.2 [328 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libpixman-1-0 armhf 0.36.0-1 [458 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.8-1+b2 [19.1 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-2 [135 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.6.12-1 [311 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.6.12-1 [700 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libxcb-render0 armhf 1.14-2 [110 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libxcb-shm0 armhf 1.14-2 [101 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1+b2 [47.8 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libxrender1 armhf 1:0.9.10-1 [29.9 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libcairo2 armhf 1.16.0-4 [599 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libexpat1-dev armhf 2.2.10-1 [121 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libinchi1 armhf 1.03+dfsg-3 [351 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libmaeparser1 armhf 1.2.4-1 [76.1 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libopenbabel7 armhf 3.1.1+dfsg-3+b1 [2775 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9 armhf 3.9.0-5+rpi1 [1411 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-dev armhf 3.9.0-5+rpi1 [3053 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libpython3-dev armhf 3.9.0-4 [21.2 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libpython3.8-stdlib armhf 3.8.6-1 [1654 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libxml2-utils armhf 2.9.10+dfsg-6.3 [105 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf libxslt1.1 armhf 1.1.34-4 [218 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf openbabel armhf 3.1.1+dfsg-3+b1 [128 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf pkg-config armhf 0.29.2-1 [61.5 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf python3.9-dev armhf 3.9.0-5+rpi1 [501 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf python3-dev armhf 3.9.0-4 [1164 B]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf python3.8 armhf 3.8.6-1 [422 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf python3-pkg-resources all 50.3.0-1 [187 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf python3-numpy armhf 1:1.19.4-1+b1 [4142 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf scons all 4.0.1+dfsg-2 [559 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf swig4.0 armhf 4.0.2-1 [1221 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf swig all 4.0.2-1 [330 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf xsltproc armhf 1.1.34-4 [123 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf xmlto armhf 0.0.28-2.1 [32.1 kB]
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Setting up media-types (1.0.1) ...
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Setting up libpixman-1-0:armhf (0.36.0-1) ...
Setting up libxau6:armhf (1:1.0.8-1+b2) ...
Setting up libpython3.8-minimal:armhf (3.8.6-1) ...
Setting up libicu67:armhf (67.1-4) ...
Setting up libmagic-mgc (1:5.38-5) ...
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Setting up file (1:5.38-5) ...
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Setting up libasan6:armhf (10.2.0-19+rpi1) ...
Setting up libmaeparser1:armhf (1.2.4-1) ...
Setting up autotools-dev (20180224.1) ...
Setting up libblas3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libexpat1-dev:armhf (2.2.10-1) ...
Setting up libx11-data (2:1.6.12-1) ...
Setting up libsigsegv2:armhf (2.12-2) ...
Setting up libpng16-16:armhf (1.6.37-3) ...
Setting up libatomic1:armhf (10.2.0-19+rpi1) ...
Setting up autopoint (0.19.8.1-10) ...
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Setting up python3.8-minimal (3.8.6-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up sgml-base (1.30) ...
Setting up dos2unix (7.4.1-1) ...
Setting up swig4.0 (4.0.2-1) ...
Setting up libisl23:armhf (0.23-1) ...
Setting up libbsd0:armhf (0.10.0-1) ...
Setting up mailcap (3.67) ...
Setting up libelf1:armhf (0.182-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up libcc1-0:armhf (10.2.0-19+rpi1) ...
Setting up cpp-10 (10.2.0-19+rpi1) ...
Setting up libinchi1 (1.03+dfsg-3) ...
Setting up libfile-stripnondeterminism-perl (1.9.0-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up liblapack3:armhf (3.9.0-3) ...
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 (1.14-2) ...
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Setting up libtool (2.4.6-14) ...
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Setting up fontconfig-config (2.13.1-4.2) ...
Setting up libgcc-10-dev:armhf (10.2.0-19+rpi1) ...
Setting up m4 (1.4.18-4) ...
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Setting up libfreetype6:armhf (2.10.2+dfsg-4) ...
Setting up libcroco3:armhf (0.6.13-1) ...
Setting up gcc-10 (10.2.0-19+rpi1) ...
Setting up autoconf (2.69-11.1) ...
Setting up dh-strip-nondeterminism (1.9.0-1) ...
Setting up dwz (0.13-5) ...
Setting up groff-base (1.22.4-5) ...
Setting up xml-core (0.18+nmu1) ...
Setting up libxslt1.1:armhf (1.1.34-4) ...
Setting up libx11-6:armhf (2:1.6.12-1) ...
Setting up libgfortran-10-dev:armhf (10.2.0-19+rpi1) ...
Setting up libfontconfig1:armhf (2.13.1-4.2) ...
Setting up libpython3.8-stdlib:armhf (3.8.6-1) ...
Setting up libxml2-utils (2.9.10+dfsg-6.3) ...
Setting up python3.8 (3.8.6-1) ...
Setting up libpython3.9-stdlib:armhf (3.9.0-5+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.0-4) ...
Setting up automake (1:1.16.2-4) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up gettext (0.19.8.1-10) ...
Setting up libstdc++-10-dev:armhf (10.2.0-19+rpi1) ...
Setting up g++-10 (10.2.0-19+rpi1) ...
Setting up libxrender1:armhf (1:0.9.10-1) ...
Setting up xsltproc (1.1.34-4) ...
Setting up libxext6:armhf (2:1.3.3-1+b2) ...
Setting up man-db (2.9.3-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up libcairo2:armhf (1.16.0-4) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libpython3.9:armhf (3.9.0-5+rpi1) ...
Setting up gfortran-10 (10.2.0-19+rpi1) ...
Setting up python3.9 (3.9.0-5+rpi1) ...
Setting up po-debconf (1.0.21) ...
Setting up libpython3.9-dev:armhf (3.9.0-5+rpi1) ...
Setting up libopenbabel7 (3.1.1+dfsg-3+b1) ...
Setting up python3 (3.9.0-4) ...
Setting up gfortran (4:10.2.0-1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up python3.9-dev (3.9.0-5+rpi1) ...
Setting up python3-lib2to3 (3.8.6-1) ...
Setting up python3-pkg-resources (50.3.0-1) ...
Setting up python3-distutils (3.8.6-1) ...
Setting up dh-python (4.20201102) ...
Setting up libpython3-dev:armhf (3.9.0-4) ...
Setting up openbabel (3.1.1+dfsg-3+b1) ...
Setting up python3-dev (3.9.0-4) ...
Setting up scons (4.0.1+dfsg-2) ...
Setting up python3-numpy (1:1.19.4-1+b1) ...
Setting up dh-autoreconf (19) ...
Setting up debhelper (13.2.1) ...
Processing triggers for libc-bin (2.31-4+rpi1) ...
Processing triggers for sgml-base (1.30) ...
Setting up docbook-xsl (1.79.2+dfsg-1) ...
Setting up sgml-data (2.0.11) ...
Processing triggers for sgml-base (1.30) ...
Setting up docbook-xml (4.5-9) ...
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) ...
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.1-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.1-2+rpi1 dpkg-dev_1.20.5+rpi1 g++-10_10.2.0-19+rpi1 gcc-10_10.2.0-19+rpi1 libc6-dev_2.31-4+rpi1 libstdc++-10-dev_10.2.0-19+rpi1 libstdc++6_10.2.0-19+rpi1 linux-libc-dev_5.7.10-1+rpi1
Package versions: adduser_3.118 apt_2.1.10 aptitude_0.8.13-2 aptitude-common_0.8.13-2 autoconf_2.69-11.1 automake_1:1.16.2-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11+rpi1 base-passwd_3.5.48 bash_5.1~rc1-2 binutils_2.35.1-2+rpi1 binutils-arm-linux-gnueabihf_2.35.1-2+rpi1 binutils-common_2.35.1-2+rpi1 bsdextrautils_2.36-3 bsdutils_1:2.36-3 build-essential_12.8 bzip2_1.0.8-4 coreutils_8.32-4 cpp_4:10.2.0-1+rpi1 cpp-10_10.2.0-19+rpi1 dash_0.5.10.2-7 debconf_1.5.74 debhelper_13.2.1 debianutils_4.11.2 dh-autoreconf_19 dh-python_4.20201102 dh-strip-nondeterminism_1.9.0-1 diffutils_1:3.7-3 dirmngr_2.2.20-1 docbook-xml_4.5-9 docbook-xsl_1.79.2+dfsg-1 dos2unix_7.4.1-1 dpkg_1.20.5+rpi1 dpkg-dev_1.20.5+rpi1 dwz_0.13-5 e2fsprogs_1.45.6-1 fakeroot_1.25.3-1 fdisk_2.36-3 file_1:5.38-5 findutils_4.7.0-1 fontconfig-config_2.13.1-4.2 fonts-dejavu-core_2.37-2 g++_4:10.2.0-1+rpi1 g++-10_10.2.0-19+rpi1 gcc_4:10.2.0-1+rpi1 gcc-10_10.2.0-19+rpi1 gcc-10-base_10.2.0-19+rpi1 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gfortran_4:10.2.0-1+rpi1 gfortran-10_10.2.0-19+rpi1 gnupg_2.2.20-1 gnupg-l10n_2.2.20-1 gnupg-utils_2.2.20-1 gpg_2.2.20-1 gpg-agent_2.2.20-1 gpg-wks-client_2.2.20-1 gpg-wks-server_2.2.20-1 gpgconf_2.2.20-1 gpgsm_2.2.20-1 gpgv_2.2.20-1 grep_3.4-1 groff-base_1.22.4-5 gzip_1.10-2 hostname_3.23 init-system-helpers_1.58 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20200821-2 krb5-locales_1.17-10 libacl1_2.2.53-8 libalgorithm-diff-perl_1.200-1 libalgorithm-merge-perl_0.08-3 libapt-pkg6.0_2.1.10 libarchive-zip-perl_1.68-1 libasan6_10.2.0-19+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.0-19+rpi1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-3.1 libaudit1_1:2.8.5-3.1 libbinutils_2.35.1-2+rpi1 libblas3_3.9.0-3 libblkid1_2.36-3 libboost-iostreams1.71.0_1.71.0-7 libbrotli1_1.0.9-2+b1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-4+rpi1 libc-dev-bin_2.31-4+rpi1 libc6_2.31-4+rpi1 libc6-dev_2.31-4+rpi1 libcairo2_1.16.0-4 libcap-ng0_0.7.9-2.2 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcc1-0_10.2.0-19+rpi1 libcom-err2_1.45.6-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.1-2+rpi1 libctf0_2.35.1-2+rpi1 libcwidget4_0.5.18-5 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.254 libdebhelper-perl_13.2.1 libdpkg-perl_1.20.5+rpi1 libelf1_0.182-1 libexpat1_2.2.10-1 libexpat1-dev_2.2.10-1 libext2fs2_1.45.6-1 libfakeroot_1.25.3-1 libfdisk1_2.36-3 libffi7_3.3-4 libfile-stripnondeterminism-perl_1.9.0-1 libfontconfig1_2.13.1-4.2 libfreetype6_2.10.2+dfsg-4 libgcc-10-dev_10.2.0-19+rpi1 libgcc-s1_10.2.0-19+rpi1 libgcrypt20_1.8.6-2 libgdbm-compat4_1.18.1-5.1 libgdbm6_1.18.1-5.1 libgfortran-10-dev_10.2.0-19+rpi1 libgfortran5_10.2.0-19+rpi1 libglib2.0-0_2.66.3-2 libgmp10_2:6.2.0+dfsg-6 libgnutls30_3.6.15-4 libgomp1_10.2.0-19+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.17-10+b3 libhogweed6_3.6-2 libicu67_67.1-4 libidn2-0_2.3.0-1 libinchi1_1.03+dfsg-3 libisl22_0.22.1-1 libisl23_0.23-1 libk5crypto3_1.17-10+b3 libkeyutils1_1.6.1-2 libkrb5-3_1.17-10+b3 libkrb5support0_1.17-10+b3 libksba8_1.4.0-2 liblapack3_3.9.0-3 libldap-2.4-2_2.4.53+dfsg-1+rpi1 libldap-common_2.4.53+dfsg-1+rpi1 liblocale-gettext-perl_1.07-4+b1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1 libmaeparser1_1.2.4-1 libmagic-mgc_1:5.38-5 libmagic1_1:5.38-5 libmount1_2.36-3 libmpc3_1.2.0-1 libmpfr6_4.1.0-3 libncursesw6_6.2+20200918-1 libnettle8_3.6-2 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libopenbabel7_3.1.1+dfsg-3+b1 libp11-kit0_0.23.21-2 libpam-cap_1:2.44-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-13 libperl5.32_5.32.0-5 libpipeline1_1.5.3-1 libpixman-1-0_0.36.0-1 libpng16-16_1.6.37-3 libpython3-dev_3.9.0-4 libpython3-stdlib_3.9.0-4 libpython3.8-minimal_3.8.6-1 libpython3.8-stdlib_3.8.6-1 libpython3.9_3.9.0-5+rpi1 libpython3.9-dev_3.9.0-5+rpi1 libpython3.9-minimal_3.9.0-5+rpi1 libpython3.9-stdlib_3.9.0-5+rpi1 libreadline8_8.0-4 libsasl2-2_2.1.27+dfsg-2 libsasl2-modules-db_2.1.27+dfsg-2 libseccomp2_2.4.4-1+rpi1 libselinux1_3.1-2 libsemanage-common_3.1-1 libsemanage1_3.1-1 libsepol1_3.1-1 libsigc++-2.0-0v5_2.10.4-2 libsigsegv2_2.12-2 libsmartcols1_2.36-3 libsqlite3-0_3.33.0-1 libss2_1.45.6-1 libssl1.1_1.1.1g-1 libstdc++-10-dev_10.2.0-19+rpi1 libstdc++6_10.2.0-19+rpi1 libsub-override-perl_0.09-2 libsystemd0_246.4-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20200918-1 libtirpc-common_1.2.6-3 libtirpc-dev_1.2.6-3 libtirpc3_1.2.6-3 libtool_2.4.6-14 libubsan1_10.2.0-19+rpi1 libuchardet0_0.0.7-1 libudev1_246.4-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36-3 libx11-6_2:1.6.12-1 libx11-data_2:1.6.12-1 libxapian30_1.4.17-1 libxau6_1:1.0.8-1+b2 libxcb-render0_1.14-2 libxcb-shm0_1.14-2 libxcb1_1.14-2 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1+b2 libxml2_2.9.10+dfsg-6.3 libxml2-utils_2.9.10+dfsg-6.3 libxrender1_1:0.9.10-1 libxslt1.1_1.1.34-4 libzstd1_1.4.5+dfsg-4+rpi1 linux-libc-dev_5.7.10-1+rpi1 login_1:4.8.1-1 logsave_1.45.6-1 lsb-base_11.1.0+rpi1 m4_1.4.18-4 mailcap_3.67 make_4.3-4 man-db_2.9.3-2 mawk_1.3.4.20200120-2 media-types_1.0.1 mime-support_3.66 mount_2.36-3 ncurses-base_6.2+20200918-1 ncurses-bin_6.2+20200918-1 netbase_6.2 openbabel_3.1.1+dfsg-3+b1 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.32.0-5 perl-base_5.32.0-5 perl-modules-5.32_5.32.0-5 pinentry-curses_1.1.0-4 pkg-config_0.29.2-1 po-debconf_1.0.21 python3_3.9.0-4 python3-dev_3.9.0-4 python3-distutils_3.8.6-1 python3-lib2to3_3.8.6-1 python3-minimal_3.9.0-4 python3-numpy_1:1.19.4-1+b1 python3-pkg-resources_50.3.0-1 python3.8_3.8.6-1 python3.8-minimal_3.8.6-1 python3.9_3.9.0-5+rpi1 python3.9-dev_3.9.0-5+rpi1 python3.9-minimal_3.9.0-5+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.0-4 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-pdb2pqr-dummy_0.invalid.0 scons_4.0.1+dfsg-2 sed_4.7-1 sensible-utils_0.0.12+nmu1 sgml-base_1.30 sgml-data_2.0.11 swig_4.0.2-1 swig4.0_4.0.2-1 sysvinit-utils_2.96-5 tar_1.30+dfsg-7 tzdata_2020d-1 ucf_3.0043 util-linux_2.36-3 xml-core_0.18+nmu1 xmlto_0.0.28-2.1 xsltproc_1.1.34-4 xz-utils_5.2.4-1 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.mYHPHx7_/trustedkeys.kbx': General error
gpgv: Signature made Sun Mar 29 16:06:48 2020 UTC
gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
gpgv: issuer "tille@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./pdb2pqr_2.1.1+dfsg-7.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-7.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
Hack binNMU version
-------------------
Created changelog entry for binNMU version 2.1.1+dfsg-7+b1
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-90002195-3678-4524-a2c0-a9e621e56f7b
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package pdb2pqr
dpkg-buildpackage: info: source version 2.1.1+dfsg-7+b1
dpkg-buildpackage: info: source distribution bullseye-staging
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:1822,
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
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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_vector.h:558:31: 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++/10/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++/10/bits/stl_vector.h:1198:21: 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++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/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++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:121:21: 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++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
346 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/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++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
107 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:109:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
109 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_algobase.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 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:569:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
568 | return std::__copy_move_a<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algobase.h:61,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/cpp_type_traits.h:544:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
544 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:511:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
511 | __copy_move_a(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:511:5: 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++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
107 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:109:27: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
109 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algobase.h:67,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_iterator.h:1225:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1225 | __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
560 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algobase.h:67,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from pdb2pka/pMC_mult.h:9,
from pdb2pka/pMC_mult.cpp:6:
/usr/include/c++/10/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++/10/bits/stl_iterator.h:2202:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
2202 | __miter_base(move_iterator<_Iterator> __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:4847:171: 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:4848:218: 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:4849:219: 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:4850:223: 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:8847:60: 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:8897:65: 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:9288:83: 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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_vector.h:558:31: 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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1198:21: 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++/10/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++/10/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++/10/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++/10/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++/10/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++/10/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++/10/bits/stl_vector.h:1461:17: 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++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/bits/vector.tcc:154:19: 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++/10/bits/vector.tcc:161:19: 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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/bits/stl_vector.h:1338:16: 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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/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++/10/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++/10/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++/10/bits/stl_vector.h:960:18: 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++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::reserve(std::vector<_Tp, _Alloc>::size_type) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:85:36: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
85 | __tmp = _M_allocate_and_copy(__n,
| ~~~~~~~~~~~~~~~~~~~~^~~~~
86 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(this->_M_impl._M_start),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
87 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(this->_M_impl._M_finish));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/vector.tcc:226:44: 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++/10/bits/vector.tcc:238:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
238 | std::_Destroy(std::copy(__x.begin(), __x.end(), begin()),
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
239 | end(), _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:238:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
325 | { 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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_vector.h:653:2: 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++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:657:23: 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++/10/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++/10/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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.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 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:569:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
568 | return std::__copy_move_a<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1379:2: 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++/10/bits/stl_vector.h:1379:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1379:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1383:22: 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++/10/bits/stl_vector.h:1383:22: 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++/10/bits/stl_algobase.h:67,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/bits/stl_iterator.h: In constructor 'std::reverse_iterator<_Iterator>::reverse_iterator(std::reverse_iterator<_Iterator>::iterator_type) [with _Iterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/10/bits/stl_iterator.h:167:7: 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
167 | reverse_iterator(iterator_type __x) : current(__x) { }
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/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++/10/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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/bits/vector.tcc:175:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
175 | _GLIBCXX_MOVE3(__position + 1, end(), __position);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/bits/vector.tcc:190:6: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
190 | _GLIBCXX_MOVE3(__last, end(), __first);
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/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++/10/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++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/vector.tcc:267:13: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
267 | std::fill(begin(), end(), __val);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/bits/stl_vector.h: In member function 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(std::vector<_Tp, _Alloc>::size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = std::move_iterator<double*>; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:1508:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
1508 | _M_allocate_and_copy(size_type __n,
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1508:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1514:35: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
1514 | std::__uninitialized_copy_a(__first, __last, __result,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
1515 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_vector.h:1508:2: 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++/10/bits/stl_vector.h:1508:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1514:35: 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++/10/ext/alloc_traits.h:34,
from /usr/include/c++/10/bits/basic_string.h:40,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/alloc_traits.h:735:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
735 | _Destroy(_ForwardIterator __first, _ForwardIterator __last,
| ^~~~~~~~
/usr/include/c++/10/bits/alloc_traits.h:735:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/alloc_traits.h:738:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
738 | _Destroy(__first, __last);
| ~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1577:2: 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++/10/bits/stl_vector.h:1577:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1580:39: 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++/10/bits/stl_vector.h:1585:33: 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++/10/bits/stl_algobase.h:67,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/bits/stl_iterator.h: In constructor 'std::reverse_iterator<_Iterator>::reverse_iterator(std::reverse_iterator<_Iterator>::iterator_type) [with _Iterator = __gnu_cxx::__normal_iterator<const double*, std::vector<double> >]':
/usr/include/c++/10/bits/stl_iterator.h:167:7: 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
167 | reverse_iterator(iterator_type __x) : current(__x) { }
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/cmath:42,
from /usr/include/c++/10/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:63,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/10/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++/10/bits/cpp_type_traits.h:544:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
544 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:511:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
511 | __copy_move_a(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:511:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:511:5: 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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_vector.h:1662:2: 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++/10/bits/stl_vector.h:1662:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1662:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1665:19: 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++/10/bits/stl_vector.h:1665:19: 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++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:347:2: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
346 | return std::__uninitialized_copy_a
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
347 | (_GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__first),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
348 | _GLIBCXX_MAKE_MOVE_IF_NOEXCEPT_ITERATOR(__last), __result, __alloc);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:593:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
593 | move(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:593:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:593:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:601:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
601 | return std::__copy_move_a<true>(std::__miter_base(__first),
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
602 | std::__miter_base(__last), __result);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:333:41: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
333 | return std::__uninitialized_copy_a(_GLIBCXX_MAKE_MOVE_ITERATOR(__first),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
334 | _GLIBCXX_MAKE_MOVE_ITERATOR(__last),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
335 | __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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
937 | fill(_ForwardIterator __first, _ForwardIterator __last, const _Tp& __value)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:937:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:944:20: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
944 | std::__fill_a(__first, __last, __value);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
323 | __uninitialized_copy_a(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:323:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:325:37: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
325 | { return std::uninitialized_copy(__first, __last, __result); }
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/alloc_traits.h:33,
from /usr/include/c++/10/ext/alloc_traits.h:34,
from /usr/include/c++/10/bits/basic_string.h:40,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/bits/stl_construct.h: In function 'void std::_Destroy(_ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >]':
/usr/include/c++/10/bits/stl_construct.h:171:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
171 | _Destroy(_ForwardIterator __first, _ForwardIterator __last)
| ^~~~~~~~
/usr/include/c++/10/bits/stl_construct.h:171:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_construct.h:185:11: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
184 | std::_Destroy_aux<__has_trivial_destructor(_Value_type)>::
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | __destroy(__first, __last);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
107 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:109:27: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
109 | { 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++/10/bits/stl_algobase.h:66,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/bits/stl_iterator_base_funcs.h: In function '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++/10/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++/10/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++/10/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++/10/bits/stl_algobase.h:67,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_iterator.h:1225:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
1225 | __niter_base(__gnu_cxx::__normal_iterator<_Iterator, _Container> __it)
| ^~~~~~~~~~~~
/usr/include/c++/10/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++/10/bits/stl_iterator.h:1225:5: 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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:323:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
323 | __niter_wrap(_From __from, _To __res)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/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++/10/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++/10/bits/vector.tcc:727:41: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
727 | const size_type __n = std::distance(__first, __last);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:744:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
744 | std::copy(__first, __last, __position);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:751:34: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
751 | std::__uninitialized_copy_a(__mid, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
752 | this->_M_impl._M_finish,
| ~~~~~~~~~~~~~~~~~~~~~~~~
753 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:762:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
762 | std::copy(__first, __mid, __position);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:778:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
778 | = std::__uninitialized_copy_a(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
779 | __new_finish,
| ~~~~~~~~~~~~~
780 | _M_get_Tp_allocator());
| ~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/cmath:42,
from /usr/include/c++/10/math.h:36,
from /usr/include/python3.9/pyport.h:205,
from /usr/include/python3.9/Python.h:63,
from pdb2pka/pMC_mult_wrap.cpp:178:
/usr/include/c++/10/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++/10/bits/cpp_type_traits.h:544:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
544 | __miter_base(_Iterator __it)
| ^~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:511:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
511 | __copy_move_a(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:511:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:511:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
pdb2pka/pMC_mult_wrap.cpp: In function 'void swig::assign(const SwigPySeq&, Seq*) [with SwigPySeq = swig::SwigPySequence_Cont<double>; Seq = std::vector<double>]':
pdb2pka/pMC_mult_wrap.cpp: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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:913:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
913 | __fill_a(_FIte __first, _FIte __last, const _Tp& __value)
| ^~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:913:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:914:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
914 | { std::__fill_a1(__first, __last, __value); }
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/bits/stl_uninitialized.h: In function '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = std::move_iterator<double*>; _ForwardIterator = double*]':
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
125 | uninitialized_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:125:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:150:15: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
147 | return std::__uninitialized_copy<__is_trivial(_ValueType1)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
148 | && __is_trivial(_ValueType2)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
149 | && __assignable>::
| ~~~~~~~~~~~~~~~~~~
150 | __uninit_copy(__first, __last, __result);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/alloc_traits.h:33,
from /usr/include/c++/10/ext/alloc_traits.h:34,
from /usr/include/c++/10/bits/basic_string.h:40,
from /usr/include/c++/10/string:55,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_construct.h:161:9: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
161 | __destroy(_ForwardIterator, _ForwardIterator) { }
| ^~~~~~~~~
/usr/include/c++/10/bits/stl_construct.h:161:9: 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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.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 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algobase.h:569:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
568 | return std::__copy_move_a<__is_move_iterator<_II>::__value>
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | (std::__miter_base(__first), std::__miter_base(__last), __result);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/stl_algobase.h:66,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/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++/10/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++/10/vector:67,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:899:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
899 | __fill_a1(::__gnu_cxx::__normal_iterator<_Ite, _Cont> __first,
| ^~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:899:5: 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++/10/vector:66,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
107 | __uninit_copy(_InputIterator __first, _InputIterator __last,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_uninitialized.h:107:9: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
/usr/include/c++/10/bits/stl_uninitialized.h:109:27: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
109 | { return std::copy(__first, __last, __result); }
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_algobase.h:511:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const double*, std::vector<double> >' changed in GCC 7.1
511 | __copy_move_a(_II __first, _II __last, _OI __result)
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algobase.h:511:5: 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++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/bits/vector.tcc:354:17: 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++/10/bits/vector.tcc:356:19: 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++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/bits/stl_algobase.h: In function '_OI std::copy(_II, _II, _OI) [with _II = std::move_iterator<double*>; _OI = double*]':
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
560 | copy(_II __first, _II __last, _OI __result)
| ^~~~
/usr/include/c++/10/bits/stl_algobase.h:560:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from pdb2pka/pMC_mult.h:10,
from pdb2pka/pMC_mult_wrap.cpp:2815:
/usr/include/c++/10/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++/10/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++/10/bits/stl_algobase.h:67,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/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++/10/bits/stl_iterator.h:2202:5: note: parameter passing for argument of type 'std::move_iterator<double*>' changed in GCC 7.1
2202 | __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:3990:22: 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++/10/bits/stl_algobase.h:66,
from /usr/include/c++/10/bits/char_traits.h:39,
from /usr/include/c++/10/string:40,
from /usr/include/c++/10/stdexcept:39,
from pdb2pka/pMC_mult_wrap.cpp:2742:
/usr/include/c++/10/bits/stl_iterator_base_funcs.h: In function '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++/10/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++/10/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++/10/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++/10/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++/10/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++/10/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
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_testroot -a
dh_prep -a
dh_installdirs -a
debian/rules override_dh_install-arch
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_install -a
dos2unix debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py
dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/propka30/propka.py to Unix format...
dos2unix debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py
dos2unix: converting file debian/pdb2pqr/usr/share/pdb2pqr/src/psize.py to Unix format...
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installdocs -a
debian/rules override_dh_installchangelogs
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installchangelogs ChangeLog.md
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
debian/rules override_dh_installexamples
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installexamples
for bakerdoc in $( grep -l "http://agave.wustl.edu/css/baker.css" -R debian/pdb2pqr-doc/usr/share/doc/pdb2pqr/* ); do \
sed "s|href=\"http://agave.wustl.edu/css/baker.css\"|href=\"baker.css\"|g" -i $bakerdoc; done
grep: debian/pdb2pqr-doc/usr/share/doc/pdb2pqr/*: No such file or directory
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
debian/rules override_dh_installman-arch
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_installman -a
xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/pdb2pqr.1.xml
Note: Writing pdb2pqr.1
xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/psize.1.xml
Note: Writing psize.1
xmlto -o debian/pdb2pqr/usr/share/man/man1/ man debian/propka.1.xml
Note: Writing propka.1
make[1]: Leaving directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_python3 -a
dh_perl -a
debian/rules override_dh_link-arch
make[1]: Entering directory '/<<BUILDDIR>>/pdb2pqr-2.1.1+dfsg'
dh_link -a
dh_link -a usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-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-7+b1_armhf.deb'.
dpkg-deb: building package 'pdb2pqr' in '../pdb2pqr_2.1.1+dfsg-7+b1_armhf.deb'.
dpkg-genbuildinfo --build=any
dpkg-genchanges --build=any -mRaspbian wandboard test autobuilder <root@raspbian.org> >../pdb2pqr_2.1.1+dfsg-7+b1_armhf.changes
dpkg-genchanges: info: binary-only arch-specific upload (source code and arch-indep packages not included)
dpkg-source --after-build .
dpkg-buildpackage: info: binary-only upload (no source included)
--------------------------------------------------------------------------------
Build finished at 2020-12-07T21:41:49Z
Finished
--------
I: Built successfully
+------------------------------------------------------------------------------+
| Post Build Chroot |
+------------------------------------------------------------------------------+
+------------------------------------------------------------------------------+
| Changes |
+------------------------------------------------------------------------------+
pdb2pqr_2.1.1+dfsg-7+b1_armhf.changes:
--------------------------------------
Format: 1.8
Date: Sun, 29 Mar 2020 18:03:49 +0200
Source: pdb2pqr (2.1.1+dfsg-7)
Binary: pdb2pqr pdb2pqr-dbgsym
Binary-Only: yes
Architecture: armhf
Version: 2.1.1+dfsg-7+b1
Distribution: bullseye-staging
Urgency: low
Maintainer: Raspbian wandboard test autobuilder <root@raspbian.org>
Changed-By: Raspbian wandboard test autobuilder <root@raspbian.org>
Description:
pdb2pqr - Preparation of protein structures for electrostatics calculations
Changes:
pdb2pqr (2.1.1+dfsg-7+b1) bullseye-staging; urgency=low, binary-only=yes
.
* Binary-only non-maintainer upload for armhf; no source changes.
* rebuild due to debcheck failure
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Checksums-Sha256:
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c55560d86e26e189ec06eaa7e167e1fdf3d8d42baf3a10f05239fed9192884b7 7463 pdb2pqr_2.1.1+dfsg-7+b1_armhf.buildinfo
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Files:
f21cdc7590dec09b39a2cbdd839a6658 297184 debug optional pdb2pqr-dbgsym_2.1.1+dfsg-7+b1_armhf.deb
ef33e3ffcc3d8fb39368488a650c9664 7463 science optional pdb2pqr_2.1.1+dfsg-7+b1_armhf.buildinfo
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+------------------------------------------------------------------------------+
| Package contents |
+------------------------------------------------------------------------------+
pdb2pqr-dbgsym_2.1.1+dfsg-7+b1_armhf.deb
----------------------------------------
new Debian package, version 2.0.
size 297184 bytes: control archive=652 bytes.
442 bytes, 12 lines control
299 bytes, 3 lines md5sums
Package: pdb2pqr-dbgsym
Source: pdb2pqr (2.1.1+dfsg-7)
Version: 2.1.1+dfsg-7+b1
Auto-Built-Package: debug-symbols
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 529
Depends: pdb2pqr (= 2.1.1+dfsg-7+b1)
Section: debug
Priority: optional
Description: debug symbols for pdb2pqr
Build-Ids: 5503f9865b0b9ea511b33a6f09899d163f6150bd dff6291b98e4d7b07830a0f050851e8f1ba69ad9
drwxr-xr-x root/root 0 2020-03-29 16:03 ./
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/debug/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/debug/.build-id/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/debug/.build-id/55/
-rw-r--r-- root/root 498012 2020-03-29 16:03 ./usr/lib/debug/.build-id/55/03f9865b0b9ea511b33a6f09899d163f6150bd.debug
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/debug/.build-id/df/
-rw-r--r-- root/root 14956 2020-03-29 16:03 ./usr/lib/debug/.build-id/df/f6291b98e4d7b07830a0f050851e8f1ba69ad9.debug
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/debug/.dwz/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/
-rw-r--r-- root/root 14192 2020-03-29 16:03 ./usr/lib/debug/.dwz/arm-linux-gnueabihf/pdb2pqr.debug
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/share/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/share/doc/
lrwxrwxrwx root/root 0 2020-03-29 16:03 ./usr/share/doc/pdb2pqr-dbgsym -> pdb2pqr
pdb2pqr_2.1.1+dfsg-7+b1_armhf.deb
---------------------------------
new Debian package, version 2.0.
size 372192 bytes: control archive=4836 bytes.
1444 bytes, 29 lines control
9769 bytes, 131 lines md5sums
275 bytes, 12 lines * postinst #!/bin/sh
388 bytes, 12 lines * prerm #!/bin/sh
Package: pdb2pqr
Source: pdb2pqr (2.1.1+dfsg-7)
Version: 2.1.1+dfsg-7+b1
Architecture: armhf
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size: 2846
Depends: libc6 (>= 2.29), libgcc-s1 (>= 3.5), libstdc++6 (>= 5.2), 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.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
Description: Preparation of protein structures for electrostatics calculations
PDB2PQR is a Python software package that automates many of the common
tasks of preparing structures for continuum electrostatics calculations.
It thus provides a platform-independent utility for converting protein files
in PDB format to PQR format. These tasks include:
* Adding a limited number of missing heavy atoms to biomolecular structures
* Determining side-chain pKas
* Placing missing hydrogens
* Optimizing the protein for favorable hydrogen bonding
* Assigning charge and radius parameters from a variety of force fields
.
This package also includes PropKa, a tool to modify the protonation state of
protein structures in the Protein Data Bank (PDB) format to match a given pKa
value. It can also be used to refine NMR structures, which often yield
inaccurate pKa values for some residues.
drwxr-xr-x root/root 0 2020-03-29 16:03 ./
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/bin/
lrwxrwxrwx root/root 0 2020-03-29 16:03 ./usr/bin/pdb2pqr -> ../share/pdb2pqr/pdb2pqr.py
lrwxrwxrwx root/root 0 2020-03-29 16:03 ./usr/bin/propka -> ../share/pdb2pqr/propka30/propka.py
lrwxrwxrwx root/root 0 2020-03-29 16:03 ./usr/bin/psize -> ../share/pdb2pqr/src/psize.py
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/pdb2pqr/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/pdb2pqr/pdb2pka/
-rw-r--r-- root/root 582612 2020-03-29 16:03 ./usr/lib/pdb2pqr/pdb2pka/_pMC_mult.cpython-39-arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/lib/pdb2pqr/pdb2pka/substruct/
-rw-r--r-- root/root 14620 2020-03-29 16:03 ./usr/lib/pdb2pqr/pdb2pka/substruct/Algorithms.cpython-39-arm-linux-gnueabihf.so
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/share/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/share/doc/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/share/doc/pdb2pqr/
-rw-r--r-- root/root 31 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/AUTHORS
-rw-r--r-- root/root 175 2016-02-18 19:56 ./usr/share/doc/pdb2pqr/NEWS.gz
-rw-r--r-- root/root 783 2020-03-29 16:03 ./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 226 2020-03-29 16:03 ./usr/share/doc/pdb2pqr/changelog.Debian.armhf.gz
-rw-r--r-- root/root 2593 2020-03-29 16:03 ./usr/share/doc/pdb2pqr/changelog.Debian.gz
-rw-r--r-- root/root 613 2016-03-08 20:40 ./usr/share/doc/pdb2pqr/changelog.gz
-rw-r--r-- root/root 5186 2020-03-29 16:03 ./usr/share/doc/pdb2pqr/copyright
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/share/man/
drwxr-xr-x root/root 0 2020-03-29 16:03 ./usr/share/man/man1/
-rw-r--r-- root/root 2082 2020-03-29 16:03 ./usr/share/man/man1/pdb2pqr.1.gz
-rw-r--r-- root/root 1044 2020-03-29 16:03 ./usr/share/man/man1/propka.1.gz
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| Summary |
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Build Architecture: armhf
Build-Space: 56852
Build-Time: 115
Distribution: bullseye-staging
Host Architecture: armhf
Install-Time: 1182
Job: pdb2pqr_2.1.1+dfsg-7
Machine Architecture: armhf
Package: pdb2pqr
Package-Time: 1359
Source-Version: 2.1.1+dfsg-7
Space: 56852
Status: successful
Version: 2.1.1+dfsg-7+b1
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Finished at 2020-12-07T21:41:49Z
Build needed 00:22:39, 56852k disc space